TinkerTools / poltype2

Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA

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Experimenting: Psi4 segfault #11

Closed BJWiley233 closed 1 year ago

BJWiley233 commented 2 years ago

I think I am running out of memory even with 392GB for running standard pipeline for molecules size of ribociclib (62 atoms). The input for python poltype.py is:

structure=ribociclib.sdf
scratchpath=/scratch1/fs1/bolton/brian
cpujobsonly=False
numproc=16

It errors for Psi4 step with forrtl: severe (174): SIGSEGV, segmentation fault occurred and here is trace:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
libgdma.so         00007FA8EE65B0DC  for__signal_handl     Unknown  Unknown
libpthread-2.27.s  00007FA8F5D1E980  Unknown               Unknown  Unknown
libc-2.27.so       00007FA8F4FF5C01  fseek                 Unknown  Unknown
core.cpython-38-x  00007FA8F0F65581  _ZN3psi8DFHelper1     Unknown  Unknown
core.cpython-38-x  00007FA8F0FE0610  _ZN3psi8DFHelper1     Unknown  Unknown
core.cpython-38-x  00007FA8F0FE1274  _ZN3psi8DFHelper1     Unknown  Unknown
core.cpython-38-x  00007FA8F121B435  _ZN3psi7MemDFJK13     Unknown  Unknown
core.cpython-38-x  00007FA8F3479548  Unknown               Unknown  Unknown
core.cpython-38-x  00007FA8F34795BB  Unknown               Unknown  Unknown
core.cpython-38-x  00007FA8F3061D69  Unknown               Unknown  Unknown
python3.8          000055EC0CDF0B94  PyCFunction_Call      Unknown  Unknown
python3.8          000055EC0CDFFF2E  _PyObject_MakeTpC     Unknown  Unknown
python3.8          000055EC0CE75E1E  Unknown               Unknown  Unknown
python3.8          000055EC0CE96D23  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE73CF3  _PyEval_EvalCodeW     Unknown  Unknown
python3.8          000055EC0CE75807  Unknown               Unknown  Unknown
python3.8          000055EC0CE93725  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE74F06  _PyFunction_Vecto     Unknown  Unknown
python3.8          000055EC0CE929EB  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE74F06  _PyFunction_Vecto     Unknown  Unknown
python3.8          000055EC0CE929EB  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE73CF3  _PyEval_EvalCodeW     Unknown  Unknown
python3.8          000055EC0CE750D8  _PyFunction_Vecto     Unknown  Unknown
python3.8          000055EC0CDE9DAE  PyObject_Call         Unknown  Unknown
python3.8          000055EC0CE940A8  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE73CF3  _PyEval_EvalCodeW     Unknown  Unknown
python3.8          000055EC0CE750D8  _PyFunction_Vecto     Unknown  Unknown
python3.8          000055EC0CDE9DAE  PyObject_Call         Unknown  Unknown
python3.8          000055EC0CE940A8  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE73CF3  _PyEval_EvalCodeW     Unknown  Unknown
python3.8          000055EC0CE750D8  _PyFunction_Vecto     Unknown  Unknown
python3.8          000055EC0CDE9DAE  PyObject_Call         Unknown  Unknown
python3.8          000055EC0CE940A8  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE73CF3  _PyEval_EvalCodeW     Unknown  Unknown
python3.8          000055EC0CE750D8  _PyFunction_Vecto     Unknown  Unknown
python3.8          000055EC0CE93725  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE73CF3  _PyEval_EvalCodeW     Unknown  Unknown
python3.8          000055EC0CE74D59  PyEval_EvalCodeEx     Unknown  Unknown
python3.8          000055EC0CF19B5B  PyEval_EvalCode       Unknown  Unknown
python3.8          000055EC0CF19BF3  Unknown               Unknown  Unknown
python3.8          000055EC0CF335B3  Unknown               Unknown  Unknown
python3.8          000055EC0CF37E1D  PyRun_StringFlags     Unknown  Unknown
python3.8          000055EC0CF3829F  Unknown               Unknown  Unknown
python3.8          000055EC0CDEDA5B  Unknown               Unknown  Unknown
python3.8          000055EC0CE928CF  _PyEval_EvalFrame     Unknown  Unknown
python3.8          000055EC0CE73CF3  _PyEval_EvalCodeW     Unknown  Unknown
python3.8          000055EC0CE74D59  PyEval_EvalCodeEx     Unknown  Unknown
python3.8          000055EC0CF19B5B  PyEval_EvalCode       Unknown  Unknown
python3.8          000055EC0CF19BF3  Unknown               Unknown  Unknown
python3.8          000055EC0CF335B3  Unknown               Unknown  Unknown
python3.8          000055EC0CF385D2  Unknown               Unknown  Unknown
python3.8          000055EC0CF387B2  PyRun_SimpleFileE     Unknown  Unknown
python3.8          000055EC0CF38D2D  Py_RunMain            Unknown  Unknown
python3.8          000055EC0CF38EE9  Py_BytesMain          Unknown  Unknown
libc-2.27.so       00007FA8F4F8FC87  __libc_start_main     Unknown  Unknown
python3.8          000055EC0CEAC989  Unknown               Unknown  Unknown

And this is Psi4 input:

molecule {
0 1
O -6.369787488209 0.758212450846 -0.849627614529
N -3.647767587514 0.346041302745 0.200691612299
N -1.327604539555 -0.306119339874 0.192661838416
N 6.472560499215 -0.715748777872 -0.162786953897
N -6.456741296627 2.588032900937 0.526290718055
N 0.212941995780 1.518418143018 -0.195955613549
N 9.127396724275 -1.347766501451 -0.893422154225
N 0.918049412138 -0.699071851876 0.135965102619
N 2.918384947439 -1.767575968563 0.192627516150
C -4.240385575906 -0.976507119452 0.399016865942
C -4.060331454931 -1.880938101936 -0.830552529452
C -3.644863370919 -1.754399121116 1.602318109537
C -3.998726994183 -3.283850791692 -0.230402943414
C -3.133145719845 -3.076378892798 1.015005804156
C -4.319784306597 1.547087309708 0.029047638009
C -2.306132598550 0.597674995440 0.085771223678
C -2.125794393475 1.984494853804 -0.153998843049
C -3.414472784565 2.574974789601 -0.188498172010
C -5.797694505315 1.575739591234 -0.112301589966
C -0.794736407981 2.386256776881 -0.289908639890
C -0.100274259761 0.218220026783 0.037858170427
C 7.096504336050 -1.962791795426 0.269773854776
C 7.032385997558 -0.280093120332 -1.449533726295
C 8.593618862583 -1.746767901239 0.405369562762
C 8.530068357169 -0.082185546003 -1.308834676670
C 5.059740017727 -0.683544283119 -0.116218947369
C -7.881943380461 2.734800874977 0.281134514848
C -5.936687060937 3.346927343826 1.651086244134
C 2.303577347316 -0.584145388598 0.036803644970
C 4.389853387283 0.541733108711 -0.259966094293
C 4.257203571404 -1.809675880242 0.107182846096
C 3.007874809620 0.608618377077 -0.195174448582
H -5.304337733868 -0.798421641579 0.554574269516
H -4.863438814448 -1.720545771601 -1.554666557249
H -3.106142186194 -1.646994848213 -1.312837084609
H -2.858814986670 -1.187984506441 2.105119708711
H -4.438491566846 -1.941047170607 2.333899504712
H -3.589206486951 -4.025675123925 -0.922849730912
H -5.003300788106 -3.619106059073 0.056711784981
H -3.187640405581 -3.905903874494 1.726787880405
H -2.088900931006 -2.955158582958 0.711997452229
H -3.672171947309 3.608157529994 -0.385721969334
H -0.519848426482 3.424355242060 -0.477450102798
H 6.921191307341 -2.787363824769 -0.442618945793
H 6.674110583103 -2.244185641145 1.239423729973
H 6.559384590650 0.659247663904 -1.744988029897
H 6.836527936256 -1.027738045464 -2.236996002192
H 8.767238168175 -0.994517187654 1.194174278332
H 9.071067943037 -2.683586652446 0.711700161664
H 8.707580966365 0.736362299373 -0.589606128111
H 8.953590609762 0.209989261417 -2.275712612652
H 10.139926453214 -1.245088128324 -0.831072651772
H 0.611479247647 -1.652148311440 0.308855779327
H -8.130390724767 2.225544615434 -0.647589222787
H -8.467607624332 2.296407743343 1.097619338650
H -8.124329593117 3.798421184049 0.204971098484
H -6.555140668020 3.159916080289 2.536758599417
H -4.911990779435 3.051550049424 1.862343950577
H -5.961828833470 4.420021126418 1.433307923659
H 4.965128628871 1.454782689009 -0.393539033033
H 4.691697655612 -2.798016989133 0.228555698618
H 2.476346892183 1.544415213137 -0.298967192883
}
memory 392GB
set_num_threads(16)
psi4_io.set_default_path("/scratch1/fs1/bolton/brian/psi4/Psi4-ribociclib")
set maxiter 500
set freeze_core True
set PROPERTIES_ORIGIN ["COM"]
set cubeprop_tasks ['esp']
set basis aug-cc-pVTZ
E, wfn = properties('mp2',properties=['dipole'],return_wfn=True)
cubeprop(wfn)
fchk(wfn, "ribociclib-esp.fchk")
oeprop(wfn,"GRID_ESP","WIBERG_LOWDIN_INDICES","MULLIKEN_CHARGES")
clean()

BJWiley233 commented 2 years ago

Sorry and here is the log from Psi4 failing at integral setup. Should I be using less intensive DFT basis sets?


    -----------------------------------------------------------------------
          Psi4: An Open-Source Ab Initio Electronic Structure Package
                               Psi4 1.5 release

                         Git: Rev {HEAD} e9f4d6d

    D. G. A. Smith, L. A. Burns, A. C. Simmonett, R. M. Parrish,
    M. C. Schieber, R. Galvelis, P. Kraus, H. Kruse, R. Di Remigio,
    A. Alenaizan, A. M. James, S. Lehtola, J. P. Misiewicz, M. Scheurer,
    R. A. Shaw, J. B. Schriber, Y. Xie, Z. L. Glick, D. A. Sirianni,
    J. S. O'Brien, J. M. Waldrop, A. Kumar, E. G. Hohenstein,
    B. P. Pritchard, B. R. Brooks, H. F. Schaefer III, A. Yu. Sokolov,
    K. Patkowski, A. E. DePrince III, U. Bozkaya, R. A. King,
    F. A. Evangelista, J. M. Turney, T. D. Crawford, C. D. Sherrill,
    J. Chem. Phys. 152(18) 184108 (2020). https://doi.org/10.1063/5.0006002

                            Additional Code Authors
    E. T. Seidl, C. L. Janssen, E. F. Valeev, M. L. Leininger,
    J. F. Gonthier, R. M. Richard, H. R. McAlexander, M. Saitow, X. Wang,
    P. Verma, M. H. Lechner, and A. Jiang

             Previous Authors, Complete List of Code Contributors,
                       and Citations for Specific Modules
    https://github.com/psi4/psi4/blob/master/codemeta.json
    https://github.com/psi4/psi4/graphs/contributors
    http://psicode.org/psi4manual/master/introduction.html#citing-psifour

    -----------------------------------------------------------------------

    Psi4 started on: Tuesday, 17 May 2022 08:19AM

    Process ID: 25
    Host:       compute1-exec-197.ris.wustl.edu
    PSIDATADIR: /opt/conda/envs/amoebamdpoltype/share/psi4
    Memory:     500.0 MiB
    Threads:    1

  ==> Input File <==

--------------------------------------------------------------------------
molecule {
0 1
O -6.369787488209 0.758212450846 -0.849627614529
N -3.647767587514 0.346041302745 0.200691612299
N -1.327604539555 -0.306119339874 0.192661838416
N 6.472560499215 -0.715748777872 -0.162786953897
N -6.456741296627 2.588032900937 0.526290718055
N 0.212941995780 1.518418143018 -0.195955613549
N 9.127396724275 -1.347766501451 -0.893422154225
N 0.918049412138 -0.699071851876 0.135965102619
N 2.918384947439 -1.767575968563 0.192627516150
C -4.240385575906 -0.976507119452 0.399016865942
C -4.060331454931 -1.880938101936 -0.830552529452
C -3.644863370919 -1.754399121116 1.602318109537
C -3.998726994183 -3.283850791692 -0.230402943414
C -3.133145719845 -3.076378892798 1.015005804156
C -4.319784306597 1.547087309708 0.029047638009
C -2.306132598550 0.597674995440 0.085771223678
C -2.125794393475 1.984494853804 -0.153998843049
C -3.414472784565 2.574974789601 -0.188498172010
C -5.797694505315 1.575739591234 -0.112301589966
C -0.794736407981 2.386256776881 -0.289908639890
C -0.100274259761 0.218220026783 0.037858170427
C 7.096504336050 -1.962791795426 0.269773854776
C 7.032385997558 -0.280093120332 -1.449533726295
C 8.593618862583 -1.746767901239 0.405369562762
C 8.530068357169 -0.082185546003 -1.308834676670
C 5.059740017727 -0.683544283119 -0.116218947369
C -7.881943380461 2.734800874977 0.281134514848
C -5.936687060937 3.346927343826 1.651086244134
C 2.303577347316 -0.584145388598 0.036803644970
C 4.389853387283 0.541733108711 -0.259966094293
C 4.257203571404 -1.809675880242 0.107182846096
C 3.007874809620 0.608618377077 -0.195174448582
H -5.304337733868 -0.798421641579 0.554574269516
H -4.863438814448 -1.720545771601 -1.554666557249
H -3.106142186194 -1.646994848213 -1.312837084609
H -2.858814986670 -1.187984506441 2.105119708711
H -4.438491566846 -1.941047170607 2.333899504712
H -3.589206486951 -4.025675123925 -0.922849730912
H -5.003300788106 -3.619106059073 0.056711784981
H -3.187640405581 -3.905903874494 1.726787880405
H -2.088900931006 -2.955158582958 0.711997452229
H -3.672171947309 3.608157529994 -0.385721969334
H -0.519848426482 3.424355242060 -0.477450102798
H 6.921191307341 -2.787363824769 -0.442618945793
H 6.674110583103 -2.244185641145 1.239423729973
H 6.559384590650 0.659247663904 -1.744988029897
H 6.836527936256 -1.027738045464 -2.236996002192
H 8.767238168175 -0.994517187654 1.194174278332
H 9.071067943037 -2.683586652446 0.711700161664
H 8.707580966365 0.736362299373 -0.589606128111
H 8.953590609762 0.209989261417 -2.275712612652
H 10.139926453214 -1.245088128324 -0.831072651772
H 0.611479247647 -1.652148311440 0.308855779327
H -8.130390724767 2.225544615434 -0.647589222787
H -8.467607624332 2.296407743343 1.097619338650
H -8.124329593117 3.798421184049 0.204971098484
H -6.555140668020 3.159916080289 2.536758599417
H -4.911990779435 3.051550049424 1.862343950577
H -5.961828833470 4.420021126418 1.433307923659
H 4.965128628871 1.454782689009 -0.393539033033
H 4.691697655612 -2.798016989133 0.228555698618
H 2.476346892183 1.544415213137 -0.298967192883
}
memory 392GB
set_num_threads(16)
psi4_io.set_default_path("/scratch1/fs1/bolton/brian/psi4/Psi4-ribociclib")
set maxiter 500
set freeze_core True
set PROPERTIES_ORIGIN ["COM"]
set cubeprop_tasks ['esp']
set basis aug-cc-pVTZ
E, wfn = properties('mp2',properties=['dipole'],return_wfn=True)
cubeprop(wfn)
fchk(wfn, "ribociclib-esp.fchk")
oeprop(wfn,"GRID_ESP","WIBERG_LOWDIN_INDICES","MULLIKEN_CHARGES")
clean()
--------------------------------------------------------------------------

  Memory set to 365.078 GiB by Python driver.
  Threads set to 16 by Python driver.
    SCF Algorithm Type (re)set to DF.

*** tstart() called on compute1-exec-197.ris.wustl.edu
*** at Tue May 17 08:19:25 2022

   => Loading Basis Set <=

    Name: AUG-CC-PVTZ
    Role: ORBITAL
    Keyword: BASIS
    atoms 1     entry O          line   331 file /opt/conda/envs/amoebamdpoltype/share/psi4/basis/aug-cc-pvtz.gbs
    atoms 2-9   entry N          line   285 file /opt/conda/envs/amoebamdpoltype/share/psi4/basis/aug-cc-pvtz.gbs
    atoms 10-32 entry C          line   239 file /opt/conda/envs/amoebamdpoltype/share/psi4/basis/aug-cc-pvtz.gbs
    atoms 33-62 entry H          line    40 file /opt/conda/envs/amoebamdpoltype/share/psi4/basis/aug-cc-pvtz.gbs

         ---------------------------------------------------------
                                   SCF
               by Justin Turney, Rob Parrish, Andy Simmonett
                          and Daniel G. A. Smith
                              RHF Reference
                       16 Threads, 373840 MiB Core
         ---------------------------------------------------------

  ==> Geometry <==

    Molecular point group: c1
    Full point group: C1

    Geometry (in Angstrom), charge = 0, multiplicity = 1:

       Center              X                  Y                   Z               Mass
    ------------   -----------------  -----------------  -----------------  -----------------
         O           -6.369787488209     0.758212450846    -0.849627614529    15.994914619570
         N           -3.647767587514     0.346041302745     0.200691612299    14.003074004430
         N           -1.327604539555    -0.306119339874     0.192661838416    14.003074004430
         N            6.472560499215    -0.715748777872    -0.162786953897    14.003074004430
         N           -6.456741296627     2.588032900937     0.526290718055    14.003074004430
         N            0.212941995780     1.518418143018    -0.195955613549    14.003074004430
         N            9.127396724275    -1.347766501451    -0.893422154225    14.003074004430
         N            0.918049412138    -0.699071851876     0.135965102619    14.003074004430
         N            2.918384947439    -1.767575968563     0.192627516150    14.003074004430
         C           -4.240385575906    -0.976507119452     0.399016865942    12.000000000000
         C           -4.060331454931    -1.880938101936    -0.830552529452    12.000000000000
         C           -3.644863370919    -1.754399121116     1.602318109537    12.000000000000
         C           -3.998726994183    -3.283850791692    -0.230402943414    12.000000000000
         C           -3.133145719845    -3.076378892798     1.015005804156    12.000000000000
         C           -4.319784306597     1.547087309708     0.029047638009    12.000000000000
         C           -2.306132598550     0.597674995440     0.085771223678    12.000000000000
         C           -2.125794393475     1.984494853804    -0.153998843049    12.000000000000
         C           -3.414472784565     2.574974789601    -0.188498172010    12.000000000000
         C           -5.797694505315     1.575739591234    -0.112301589966    12.000000000000
         C           -0.794736407981     2.386256776881    -0.289908639890    12.000000000000
         C           -0.100274259761     0.218220026783     0.037858170427    12.000000000000
         C            7.096504336050    -1.962791795426     0.269773854776    12.000000000000
         C            7.032385997558    -0.280093120332    -1.449533726295    12.000000000000
         C            8.593618862583    -1.746767901239     0.405369562762    12.000000000000
         C            8.530068357169    -0.082185546003    -1.308834676670    12.000000000000
         C            5.059740017727    -0.683544283119    -0.116218947369    12.000000000000
         C           -7.881943380461     2.734800874977     0.281134514848    12.000000000000
         C           -5.936687060937     3.346927343826     1.651086244134    12.000000000000
         C            2.303577347316    -0.584145388598     0.036803644970    12.000000000000
         C            4.389853387283     0.541733108711    -0.259966094293    12.000000000000
         C            4.257203571404    -1.809675880242     0.107182846096    12.000000000000
         C            3.007874809620     0.608618377077    -0.195174448582    12.000000000000
         H           -5.304337733868    -0.798421641579     0.554574269516     1.007825032230
         H           -4.863438814448    -1.720545771601    -1.554666557249     1.007825032230
         H           -3.106142186194    -1.646994848213    -1.312837084609     1.007825032230
         H           -2.858814986670    -1.187984506441     2.105119708711     1.007825032230
         H           -4.438491566846    -1.941047170607     2.333899504712     1.007825032230
         H           -3.589206486951    -4.025675123925    -0.922849730912     1.007825032230
         H           -5.003300788106    -3.619106059073     0.056711784981     1.007825032230
         H           -3.187640405581    -3.905903874494     1.726787880405     1.007825032230
         H           -2.088900931006    -2.955158582958     0.711997452229     1.007825032230
         H           -3.672171947309     3.608157529994    -0.385721969334     1.007825032230
         H           -0.519848426482     3.424355242060    -0.477450102798     1.007825032230
         H            6.921191307341    -2.787363824769    -0.442618945793     1.007825032230
         H            6.674110583103    -2.244185641145     1.239423729973     1.007825032230
         H            6.559384590650     0.659247663904    -1.744988029897     1.007825032230
         H            6.836527936256    -1.027738045464    -2.236996002192     1.007825032230
         H            8.767238168175    -0.994517187654     1.194174278332     1.007825032230
         H            9.071067943037    -2.683586652446     0.711700161664     1.007825032230
         H            8.707580966365     0.736362299373    -0.589606128111     1.007825032230
         H            8.953590609762     0.209989261417    -2.275712612652     1.007825032230
         H           10.139926453214    -1.245088128324    -0.831072651772     1.007825032230
         H            0.611479247647    -1.652148311440     0.308855779327     1.007825032230
         H           -8.130390724767     2.225544615434    -0.647589222787     1.007825032230
         H           -8.467607624332     2.296407743343     1.097619338650     1.007825032230
         H           -8.124329593117     3.798421184049     0.204971098484     1.007825032230
         H           -6.555140668020     3.159916080289     2.536758599417     1.007825032230
         H           -4.911990779435     3.051550049424     1.862343950577     1.007825032230
         H           -5.961828833470     4.420021126418     1.433307923659     1.007825032230
         H            4.965128628871     1.454782689009    -0.393539033033     1.007825032230
         H            4.691697655612    -2.798016989133     0.228555698618     1.007825032230
         H            2.476346892183     1.544415213137    -0.298967192883     1.007825032230

  Running in c1 symmetry.

  Rotational constants: A =      0.01302  B =      0.00143  C =      0.00133 [cm^-1]
  Rotational constants: A =    390.35489  B =     42.96084  C =     39.81526 [MHz]
  Nuclear repulsion = 3072.799408271997891

  Charge       = 0
  Multiplicity = 1
  Electrons    = 232
  Nalpha       = 116
  Nbeta        = 116

  ==> Algorithm <==

  SCF Algorithm Type is DF.
  DIIS enabled.
  MOM disabled.
  Fractional occupation disabled.
  Guess Type is SAD.
  Energy threshold   = 1.00e-10
  Density threshold  = 1.00e-10
  Integral threshold = 1.00e-12

  ==> Primary Basis <==

  Basis Set: AUG-CC-PVTZ
    Blend: AUG-CC-PVTZ
    Number of shells: 718
    Number of basis functions: 2162
    Number of Cartesian functions: 2510
    Spherical Harmonics?: true
    Max angular momentum: 3

   => Loading Basis Set <=

    Name: (AUG-CC-PVTZ AUX)
    Role: JKFIT
    Keyword: DF_BASIS_SCF
    atoms 1     entry O          line   286 file /opt/conda/envs/amoebamdpoltype/share/psi4/basis/aug-cc-pvtz-jkfit.gbs
    atoms 2-9   entry N          line   224 file /opt/conda/envs/amoebamdpoltype/share/psi4/basis/aug-cc-pvtz-jkfit.gbs
    atoms 10-32 entry C          line   162 file /opt/conda/envs/amoebamdpoltype/share/psi4/basis/aug-cc-pvtz-jkfit.gbs
    atoms 33-62 entry H          line    70 file /opt/conda/envs/amoebamdpoltype/share/psi4/basis/aug-cc-pvtz-jkfit.gbs

  ==> Integral Setup <==

pren commented 2 years ago

What about disk space? PSI4 dfmp2 is usually pretty good with memory but do like disk space.

You can also test by rerun PSI4 with lower basis set, e.g. 6-311++G2d,2p

From: BJWiley23 @.***> Sent: Tuesday, May 17, 2022 3:20 AM To: TinkerTools/poltype2 Cc: Subscribed Subject: [TinkerTools/poltype2] Experimenting: Psi4 segfault (Issue #11)

I think I am running out of memory even with 392GB for running standard pipeline for molecules size of ribociclib (62 atoms). The input for python poltype.py is:

structure=ribociclib.sdf scratchpath=/scratch1/fs1/bolton/brian cpujobsonly=False numproc=16

It errors for Psi4 step with forrtl: severe (174): SIGSEGV, segmentation fault occurred and here is trace:

forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source libgdma.so 00007FA8EE65B0DC for__signal_handl Unknown Unknown libpthread-2.27.s 00007FA8F5D1E980 Unknown Unknown Unknown libc-2.27.so 00007FA8F4FF5C01 fseek Unknown Unknown core.cpython-38-x 00007FA8F0F65581 _ZN3psi8DFHelper1 Unknown Unknown core.cpython-38-x 00007FA8F0FE0610 _ZN3psi8DFHelper1 Unknown Unknown core.cpython-38-x 00007FA8F0FE1274 _ZN3psi8DFHelper1 Unknown Unknown core.cpython-38-x 00007FA8F121B435 _ZN3psi7MemDFJK13 Unknown Unknown core.cpython-38-x 00007FA8F3479548 Unknown Unknown Unknown core.cpython-38-x 00007FA8F34795BB Unknown Unknown Unknown core.cpython-38-x 00007FA8F3061D69 Unknown Unknown Unknown python3.8 000055EC0CDF0B94 PyCFunction_Call Unknown Unknown python3.8 000055EC0CDFFF2E _PyObject_MakeTpC Unknown Unknown python3.8 000055EC0CE75E1E Unknown Unknown Unknown python3.8 000055EC0CE96D23 _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown python3.8 000055EC0CE75807 Unknown Unknown Unknown python3.8 000055EC0CE93725 _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE74F06 _PyFunction_Vecto Unknown Unknown python3.8 000055EC0CE929EB _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE74F06 _PyFunction_Vecto Unknown Unknown python3.8 000055EC0CE929EB _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown python3.8 000055EC0CE750D8 _PyFunction_Vecto Unknown Unknown python3.8 000055EC0CDE9DAE PyObject_Call Unknown Unknown python3.8 000055EC0CE940A8 _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown python3.8 000055EC0CE750D8 _PyFunction_Vecto Unknown Unknown python3.8 000055EC0CDE9DAE PyObject_Call Unknown Unknown python3.8 000055EC0CE940A8 _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown python3.8 000055EC0CE750D8 _PyFunction_Vecto Unknown Unknown python3.8 000055EC0CDE9DAE PyObject_Call Unknown Unknown python3.8 000055EC0CE940A8 _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown python3.8 000055EC0CE750D8 _PyFunction_Vecto Unknown Unknown python3.8 000055EC0CE93725 _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown python3.8 000055EC0CE74D59 PyEval_EvalCodeEx Unknown Unknown python3.8 000055EC0CF19B5B PyEval_EvalCode Unknown Unknown python3.8 000055EC0CF19BF3 Unknown Unknown Unknown python3.8 000055EC0CF335B3 Unknown Unknown Unknown python3.8 000055EC0CF37E1D PyRun_StringFlags Unknown Unknown python3.8 000055EC0CF3829F Unknown Unknown Unknown python3.8 000055EC0CDEDA5B Unknown Unknown Unknown python3.8 000055EC0CE928CF _PyEval_EvalFrame Unknown Unknown python3.8 000055EC0CE73CF3 _PyEval_EvalCodeW Unknown Unknown python3.8 000055EC0CE74D59 PyEval_EvalCodeEx Unknown Unknown python3.8 000055EC0CF19B5B PyEval_EvalCode Unknown Unknown python3.8 000055EC0CF19BF3 Unknown Unknown Unknown python3.8 000055EC0CF335B3 Unknown Unknown Unknown python3.8 000055EC0CF385D2 Unknown Unknown Unknown python3.8 000055EC0CF387B2 PyRun_SimpleFileE Unknown Unknown python3.8 000055EC0CF38D2D Py_RunMain Unknown Unknown python3.8 000055EC0CF38EE9 Py_BytesMain Unknown Unknown libc-2.27.so 00007FA8F4F8FC87 __libc_start_main Unknown Unknown python3.8 000055EC0CEAC989 Unknown Unknown Unknown

And this is Psi4 input:

molecule { 0 1 O -6.369787488209 0.758212450846 -0.849627614529 N -3.647767587514 0.346041302745 0.200691612299 N -1.327604539555 -0.306119339874 0.192661838416 N 6.472560499215 -0.715748777872 -0.162786953897 N -6.456741296627 2.588032900937 0.526290718055 N 0.212941995780 1.518418143018 -0.195955613549 N 9.127396724275 -1.347766501451 -0.893422154225 N 0.918049412138 -0.699071851876 0.135965102619 N 2.918384947439 -1.767575968563 0.192627516150 C -4.240385575906 -0.976507119452 0.399016865942 C -4.060331454931 -1.880938101936 -0.830552529452 C -3.644863370919 -1.754399121116 1.602318109537 C -3.998726994183 -3.283850791692 -0.230402943414 C -3.133145719845 -3.076378892798 1.015005804156 C -4.319784306597 1.547087309708 0.029047638009 C -2.306132598550 0.597674995440 0.085771223678 C -2.125794393475 1.984494853804 -0.153998843049 C -3.414472784565 2.574974789601 -0.188498172010 C -5.797694505315 1.575739591234 -0.112301589966 C -0.794736407981 2.386256776881 -0.289908639890 C -0.100274259761 0.218220026783 0.037858170427 C 7.096504336050 -1.962791795426 0.269773854776 C 7.032385997558 -0.280093120332 -1.449533726295 C 8.593618862583 -1.746767901239 0.405369562762 C 8.530068357169 -0.082185546003 -1.308834676670 C 5.059740017727 -0.683544283119 -0.116218947369 C -7.881943380461 2.734800874977 0.281134514848 C -5.936687060937 3.346927343826 1.651086244134 C 2.303577347316 -0.584145388598 0.036803644970 C 4.389853387283 0.541733108711 -0.259966094293 C 4.257203571404 -1.809675880242 0.107182846096 C 3.007874809620 0.608618377077 -0.195174448582 H -5.304337733868 -0.798421641579 0.554574269516 H -4.863438814448 -1.720545771601 -1.554666557249 H -3.106142186194 -1.646994848213 -1.312837084609 H -2.858814986670 -1.187984506441 2.105119708711 H -4.438491566846 -1.941047170607 2.333899504712 H -3.589206486951 -4.025675123925 -0.922849730912 H -5.003300788106 -3.619106059073 0.056711784981 H -3.187640405581 -3.905903874494 1.726787880405 H -2.088900931006 -2.955158582958 0.711997452229 H -3.672171947309 3.608157529994 -0.385721969334 H -0.519848426482 3.424355242060 -0.477450102798 H 6.921191307341 -2.787363824769 -0.442618945793 H 6.674110583103 -2.244185641145 1.239423729973 H 6.559384590650 0.659247663904 -1.744988029897 H 6.836527936256 -1.027738045464 -2.236996002192 H 8.767238168175 -0.994517187654 1.194174278332 H 9.071067943037 -2.683586652446 0.711700161664 H 8.707580966365 0.736362299373 -0.589606128111 H 8.953590609762 0.209989261417 -2.275712612652 H 10.139926453214 -1.245088128324 -0.831072651772 H 0.611479247647 -1.652148311440 0.308855779327 H -8.130390724767 2.225544615434 -0.647589222787 H -8.467607624332 2.296407743343 1.097619338650 H -8.124329593117 3.798421184049 0.204971098484 H -6.555140668020 3.159916080289 2.536758599417 H -4.911990779435 3.051550049424 1.862343950577 H -5.961828833470 4.420021126418 1.433307923659 H 4.965128628871 1.454782689009 -0.393539033033 H 4.691697655612 -2.798016989133 0.228555698618 H 2.476346892183 1.544415213137 -0.298967192883 } memory 392GB set_num_threads(16) psi4_io.set_default_path("/scratch1/fs1/bolton/brian/psi4/Psi4-ribociclib") set maxiter 500 set freeze_core True set PROPERTIES_ORIGIN ["COM"] set cubeprop_tasks ['esp'] set basis aug-cc-pVTZ E, wfn = properties('mp2',properties=['dipole'],return_wfn=True) cubeprop(wfn) fchk(wfn, "ribociclib-esp.fchk") oeprop(wfn,"GRID_ESP","WIBERG_LOWDIN_INDICES","MULLIKEN_CHARGES") clean()

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BJWiley233 commented 2 years ago

Ok let me try that and I will let you know. Thanks. I got Ribociclib to get past the Psi4 step by actually giving all the cpus 392GB total in LSF submission but then it failed with:

ValueError: torsion parameters are all zero torsion 402 413 417 401 0 0.0 1 0 180.0 2 0 0.0 3

Traceback is:

Traceback (most recent call last):
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 4691, in RunPoltype
    poltype.main()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2800, in main
    params= self.GenerateParameters()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 3623, in GenerateParameters
    self.CheckTorsionParameters(self.key7fname,torsionsmissing,hydtorsions)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2783, in CheckTorsionParameters
    raise ValueError("torsion parameters are all zero "+line+' path ='+os.getcwd())

misterbrandonwalker commented 2 years ago

Hey, could you zip up all files into a zip folder and send a link?

From: BJWiley23 @.> Sent: Tuesday, May 17, 2022 12:50:24 PM To: TinkerTools/poltype2 @.> Cc: Subscribed @.***> Subject: Re: [TinkerTools/poltype2] Experimenting: Psi4 segfault (Issue #11)

Ok let me try that and I will let you know. Thanks. I got Ribociclib to get past the Psi4 step by actually giving all the cpus 392GB total in LSF submission but then it failed with:

ValueError: torsion parameters are all zero torsion 402 413 417 401 0 0.0 1 0 180.0 2 0 0.0 3

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BJWiley233 commented 2 years ago

From the Temp directory? right and the SDF file?

misterbrandonwalker commented 2 years ago

Yes all files, Temp and poltype.ini file please.

On Tue, May 17, 2022 at 12:58 PM BJWiley23 @.***> wrote:

From the Temp directory? right and the SDF file?

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BJWiley233 commented 2 years ago

Ok cool. Let me know if this works. https://drive.google.com/file/d/1WS2-9ocCxVGA6_YbjesTqNP4A5sucLQh/view?usp=sharing

misterbrandonwalker commented 2 years ago

I had to request access from google drive

On Tue, May 17, 2022 at 1:06 PM BJWiley23 @.***> wrote:

Ok cool. Let me know if this works.

https://drive.google.com/file/d/1WS2-9ocCxVGA6_YbjesTqNP4A5sucLQh/view?usp=sharing

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BJWiley233 commented 2 years ago

Ok just shared. Darn, it should be able to share right away.

misterbrandonwalker commented 2 years ago

Okay it was very odd, your fragment poltype jobs were created, but then from reading the log file they were skipped and goes straight to end of poltype and sees missing torsion (because fragment jobs not started). However it seems fine when I run it. A couple of comments on the input file I saw.

structure=ribociclib.sdf scratchpath=/scratch1/fs1/bolton/brian I have removed this keyword, since for example /scratch/bdw2292 would be defined in my bashrc, then poltype is now grabbing the root directory /scratch. This way less inputs needed... cpujobsonly=False I am surprised I see this one, this is like a secret option I use for running dynamics/BAR that I dont have in docs. This will not affect poltype parameterization. numproc=16

submitlocally this one is redundant and default behaviour if "externalapi"

is not added, so I removed this keyword.

compareparameters this is only used with other keyfiles and xyz files for

parameter comparison and does not affect poltype parameterization

solvation I have added an extra line in docs under the Molecular Dynamics

Input Preperation section, suggesting to create a seperate folder with new poltype.ini file for running dynamics. I suppose we could have it run immediately after parameterization but for now I keep things seperate folders.

ligandxyzfilename=final.xyz

keyfilename=final.key

externalapi=True this keywords also requires custom modification of python

program to work with submitting jobs to some other client. The default program for this submits to my own infrastructure for job submission.

On Tue, May 17, 2022 at 1:39 PM BJWiley23 @.***> wrote:

Ok just shared. Darn, it should be able to share right away.

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BJWiley233 commented 2 years ago

Thanks for the response. I just looked at all the input parameters under poltype.py to find the cpujobsonly option. I thought maybe Poltype would try to use a GPU if available for Psi4 calculations but realize now it's only through BrianQC (I like the name 😄 ). Also on LSF don't have access to a /scratch and so I would need scratchpath/dir to be something I determine so I would just add scratchpath=/scratch1/fs1/bolton/brian and scratchdir=/scratch1/fs1/bolton/brian in my bashrc and can/should this be different than PSI_SCRATCH or does it not matter? Yes like I indicated we work in the LSF "docker" infrastructure that does actually allow for MPI node spawning yet I don't know how to do that yet. Are you planning on implementing any mpi4py? I actually wouldn't know how it works. Just know gmxapi uses it.

Also I had just commented those other ones out since I will be doing binding and solvation free energy calculations later on.

misterbrandonwalker commented 2 years ago

Of course :) . I should have been more clear. So the scratchpath, is like a way for poltype to measure how much disk space is available (previously I had a default of "/scratch" since that was root of /scratch/bdw2292/ where I write scratch files for QM jobs, but since its already defined in environment as /scratch1/fs1/bolton/brian , basically now poltype will take the root of /scratch1/fs1/bolton/brian as /scratch1/ and measure total disk space available, then a proportion of that (80%) is taken and will be distributed as the max allowed scratch for each fragment poltype job. Note however, only in gaussian is maxdisk specified where as in psi4 only scratch path is specified ( /scratch1/fs1/bolton/brian).

For the MPI, Im guessing you mean should we use that to distribute jobs? I think I designed it to be default single node only, then I didnt want to assume anything about how someones node architecture is setup. For example even if we installed that package, then every job submission client would have to support that as well? Im not sure but that is just my guess.

On Tue, May 17, 2022 at 4:40 PM BJWiley23 @.***> wrote:

Thanks for the response. I just looked at all the input parameters under poltype.py to find the cpujobsonly option. I thought maybe Poltype would try to use a GPU if available but realize now it's only through BrianQC (I like the name 😄 ). Also on LSF don't have access to a /scratch and so I would need scratchpath/dir to be something I determine so I would just add scratchpath=/scratch1/fs1/bolton/brian and scratchdir=/scratch1/fs1/bolton/brian in my bashrc and can/should this be different than PSI_SCRATCH or does it not matter? Yes like I indicated we work in the LSF "docker" infrastructure that does actually allow for MPI node spawning yet I don't know how to do that yet. Are you planning on implementing any mpi4py? I actually wouldn't know how it works. Just know gmxapi https://manual.gromacs.org/documentation/2020/gmxapi/userguide/usage.html uses it.

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BJWiley233 commented 2 years ago

Yours is as good as mine 😄 . I've only been working on LSF for little over a year and I just let GROMACs do what it wants the the MPI ranking. W.R.T to your comment about the scratch disk space. I only have access to scratch space on /scratch1/fs1/bolton where the total /scratch1 is distributed amongst all the labs at WashU and so I don't have access to all of /scratch1. Do you have suggestion of a way I might be able to alter code or input so that it only looks at total disk allocation at /scratch1/fs1/bolton being the root where our max is around 15TB?

misterbrandonwalker commented 2 years ago

Ah I see, okay I will just use the parent directory of whatever is in bashrc, that should work :) . The other way around that bypasses all the defaults is just to set maxdisk in the input file. This only affects gaussian jobs however (psi4 does not have maxdisk option) and psi4 is the QM default in poltype. I will change to parent directory instead for default.

On Tue, May 17, 2022 at 5:08 PM BJWiley23 @.***> wrote:

Yours is as good as mine 😄 . I've only been working on LSF for little over a year and I just let GROMACs do what it wants the the MPI ranking. W.R.T to your comment about the scratch disk space. I only have access to scratch space on /scratch1/fs1/bolton where the total /scratch1 is distributed amongst all the labs at WashU and so I don't have access to all of /scratch1. Do you have suggestion of a way I might be able to alter code or input so that it only looks at total disk allocation at /scratch1/fs1/bolton being the root where our max is around 15TB?

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BJWiley233 commented 2 years ago

Seems to be running at finishing as I see a final minimize being perform on final.key and final.xyz in a folder /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/15_19_Index_0 however the log seems to hang on the avgmpoles.pl script and the final.key and final.xyz are not output in the currently directory. Let me know if you want me to tar up another file. Some others are running so I can see what happens in the AM. Thanks for your help!

...
Calling: minimize 15_19_Index_0-opt-2-3-038_postQMOPTpostfit.xyz -k tmp-2-3-038_postQMOPTpostfit.key 0.1 >15_19_Index_0-opt-2-3-038_postQMOPTpostfit.out path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/15_19_Index_0/qm-torsion
Calling: analyze 15_19_Index_0-opt-2-3-038_postQMOPTpostfit.xyz_2 -k tmp-2-3-038_postQMOPTpostfit.key ed > 15_19_Index_0-opt-2-3-038_postQMOPTpostfit.alz path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/15_19_Index_0/qm-torsion
Optimization terminated successfully.
         Current function value: 0.124238
         Iterations: 17
         Function evaluations: 34
Optimization terminated successfully.
         Current function value: 0.095320
         Iterations: 16
         Function evaluations: 32
Calling: minimize -k final.key final.xyz 0.1 > Minimized_final.out path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/15_19_Index_0
Calling: superpose 15_19_Index_0.xyz_2 final.xyz_2 1 N M N 0  > 15_19_Index_0-superin.txt path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/15_19_Index_0
Calling: analyze 15_19_Index_0.xyz_2 -k final.key em | grep -A11 Charge>MMDipole.txt path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/15_19_Index_0
Wed May 18 02:52:08 2022 Normal termination: logfile=/scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/15_19_Index_0/15_19_Index_0-poltype.log path=/scratch1/fs1/bolton/brian/Ribociclib2/Temp
Calling: /opt/gdma/bin/gdma < 2_10_Index_0.gdmain > 2_10_Index_0.gdmaout path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/2_10_Index_0
Calling: poledit 1 2_10_Index_0.gdmaout /storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/ParameterFiles/amoebabio18_header.prm < 2_10_Index_0-peditin.txt path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/2_10_Index_0
Calling: potential 1 2_10_Index_0.xyz -k 2_10_Index_0_prefitmultipole.key path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/2_10_Index_0
Calling: potential 2 2_10_Index_0_fortinker.cube path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/2_10_Index_0
Calling: /storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/avgmpoles.pl 2_10_Index_0_prefitmultipole.key 2_10_Index_0.xyz 2_10_Index_0-groups.txt 2_10_Index_0.key_2 2_10_Index_0.xyz_2 401 path = /scratch1/fs1/bolton/brian/Ribociclib2/Temp/Fragments/2_10_Index_0 # hangs here

BJWiley233 commented 2 years ago

Could just be the molecule size. Fluorouracil completes entire pipeline in under a minute.

misterbrandonwalker commented 2 years ago

Hello,

Yes, any files would make things much easier for me to troubleshoot. However the molecule has finished for me. I have attached the final.key and final.xyz below.

On Tue, May 17, 2022 at 10:27 PM BJWiley23 @.***> wrote:

Could just be the molecule size. Fluorouracil completes entire pipeline in under a minute.

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BJWiley233 commented 2 years ago

Nice I got one to finish with Ribociclib. I just tested a smaller molecule and got a different traceback that I haven't seen before:

Traceback (most recent call last):
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 4670, in RunPoltype
    poltype.main()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2780, in main
    params= self.GenerateParameters()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 3589, in GenerateParameters
    torgen.gen_torsion(self,optmol,self.torsionrestraint,mol)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/torsiongenerator.py", line 844, in gen_torsion
    listoftinkertorstructures,energyarray,flatphaselist=tinker_minimize_angles(poltype,torset,optmol,variabletorlist,flatphaselist,prevstrctfname,torsionrestraint,bondtopology)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/torsiongenerator.py", line 397, in tinker_minimize_angles
    prevstrctfname,torxyzfname,newtorxyzfname,keyfname,failedcheck=tinker_minimize(poltype,torset,optmol,variabletorlist,phaseanglelist,torsionrestraint,prevstruct,'_preQMOPTprefit',poltype.key6fname,'../',torxyzfname,tmpkeyfname,torminlogfname)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/torsiongenerator.py", line 479, in tinker_minimize
    save_structfile(poltype,prevstruct,torxyzfname)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/torsiongenerator.py", line 1786, in save_structfile
    tmpfh.write( '%6d %2s %13.6f %11.6f %11.6f %5d' % (ia.GetIdx(), an.getElSymbol(ia.GetAtomicNum()), ia.x(), ia.y(), ia.z(), poltype.idxtosymclass[ia.GetIdx()]))
  File "/opt/conda/envs/amoebamdpoltype/lib/python3.8/site-packages/PyAstronomy/pyasl/asl/atomicNo.py", line 44, in getElSymbol
    raise(PE.PyAValError("No such atomic number in the data base: " + str(atn)))
PyAstronomy.pyaC.pyaErrors.pyaValErrs.PyAValError:
---------------------
A PyA error occurred:
---------------------
Type of error: PyA Value Error
What happened?
    No such atomic number in the data base: 0

BJWiley233 commented 2 years ago

Whoops you need the link... https://drive.google.com/file/d/1-N14ZLQMnJnWoCnb9D5b0hWAkmKsOUzs/view?usp=sharing

misterbrandonwalker commented 2 years ago

We just saw this issue a few days, ago try a git pull and run that one that crash with " raise(PE.PyAValError("No such atomic number in the data base: " + str(atn)))

PyAstronomy.pyaC.pyaErrors.pyaValErrs.PyAValError:" again and it should fix for you.

On Wed, May 18, 2022 at 3:55 PM BJWiley23 @.***> wrote:

Whoops you need the link...

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BJWiley233 commented 2 years ago

ah cool, yes last time I pulled was Saturday

BJWiley233 commented 2 years ago

I pulled the latest version last night and seem to be getting this type of error pretty consistently "torsion all zero". As well as "torsion set need 5 points". Don't we only need 4 points for torsions? Also getting the same "all zero torsion" error above. I am now only including molecule and numproc=16 in the poltype.ini files. Maybe you could test running the molecules indicated below for the tracebacks. Let me know if you want a tarred folder but is probably same issue as above that I linked to.

Traceback "torsion all zero" : cyclophosphamide, ZINC95080215, semaxanib, ibrutinib

Traceback (most recent call last):
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 4684, in RunPoltype
    poltype.main()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2793, in main
    params= self.GenerateParameters()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 3616, in GenerateParameters
    self.CheckTorsionParameters(self.key7fname,torsionsmissing,hydtorsions)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2776, in CheckTorsionParameters
    raise ValueError("torsion parameters are all zero "+line+' path ='+os.getcwd())
ValueError: torsion parameters are all zero torsion 405 410 411 401 0 0.0 1 0 180.0 2 0 0.0 3
 path =/scratch1/fs1/bolton/brian/cyclophosphamide/Temp

Traceback for "torsion need 5 points": carmustine,

Traceback (most recent call last):
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 4684, in RunPoltype
    poltype.main()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2793, in main
    params= self.GenerateParameters()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 3603, in GenerateParameters
    torgen.gen_torsion(self,optmol,self.torsionrestraint,mol)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/torsiongenerator.py", line 1020, in gen_torsion
    qme_list,qang_list,WBOarray,energytophaseangle = torfit.compute_qm_tor_energy(poltype,torset,optmol,flatphaselist)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/torsionfit.py", line 218, in compute_qm_tor_energy
    raise ValueError('Too many missing QM SP energy values for torsion set = '+str(torset)+' , need '+str(prmnum)+' points')
ValueError: Too many missing QM SP energy values for torsion set = ((8, 5, 7, 4),) , need 5 points

misterbrandonwalker commented 2 years ago

Could you send a zipper folder please? I’ll take a look, the missing torsion issue should be fixed as of this morning.

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From: BJWiley23 @.> Sent: Friday, May 20, 2022 3:32:36 PM To: TinkerTools/poltype2 @.> Cc: Brandon Walker @.>; Comment @.> Subject: Re: [TinkerTools/poltype2] Experimenting: Psi4 segfault (Issue #11)

I pulled the latest version last night and seem to be getting this type of error pretty consistently "torsion all zero". As well as "torsion set need 5 points". Don't we only need 4 points for torsions? Also getting the same "all zero torsion" error above. I am now only including molecule and numproc=16 in the poltype.ini files. Maybe you could test running the molecules indicated below for the tracebacks. Let me know if you want a tarred folder but is probably same issue as above that I linked to.

Traceback "torsion all zero" : cyclophosphamide, ZINC95080215, semaxanib, ibrutinib

Traceback (most recent call last): File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 4684, in RunPoltype poltype.main() File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2793, in main params= self.GenerateParameters() File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 3616, in GenerateParameters self.CheckTorsionParameters(self.key7fname,torsionsmissing,hydtorsions) File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2776, in CheckTorsionParameters raise ValueError("torsion parameters are all zero "+line+' path ='+os.getcwd()) ValueError: torsion parameters are all zero torsion 405 410 411 401 0 0.0 1 0 180.0 2 0 0.0 3 path =/scratch1/fs1/bolton/brian/cyclophosphamide/Temp

Traceback for "torsion need 5 points": carmustine,

Traceback (most recent call last): File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 4684, in RunPoltype poltype.main() File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2793, in main params= self.GenerateParameters() File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 3603, in GenerateParameters torgen.gen_torsion(self,optmol,self.torsionrestraint,mol) File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/torsiongenerator.py", line 1020, in gen_torsion qme_list,qang_list,WBOarray,energytophaseangle = torfit.compute_qm_tor_energy(poltype,torset,optmol,flatphaselist) File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/torsionfit.py", line 218, in compute_qm_tor_energy raise ValueError('Too many missing QM SP energy values for torsion set = '+str(torset)+' , need '+str(prmnum)+' points') ValueError: Too many missing QM SP energy values for torsion set = ((8, 5, 7, 4),) , need 5 points

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BJWiley233 commented 2 years ago

Sure, which one of the 2 above is the "missing torsion issue"? I will send the other as I pulled just recently. NVM i get it.

misterbrandonwalker commented 2 years ago

raise ValueError("torsion parameters are all zero "+line+' path ='+os.getcwd()) ValueError: torsion parameters are all zero torsion 405 410 411 401 0 0.0 1 0 180.0 2 0 0.0 3

this one should be fixed now

On Fri, May 20, 2022 at 4:41 PM BJWiley23 @.***> wrote:

Sure, which one of the 2 above is the "missing torsion issue"? I will send the other as I pulled just recently.

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BJWiley233 commented 2 years ago

Here you go: https://drive.google.com/file/d/1UVgwGraQz5CKLAwYKJT0WQNxU0lL3Mpe/view?usp=sharing

BJWiley233 commented 2 years ago

Most of my issues with torsion have seem to not be appear after pull last night. However now when running the binding module the first call to pdbxyz uncomplexed.pdb amoebabio18.prm will hang because, maybe it's just newest version of Tinker 8.10.2??, but you cannot input the parameter file as a command line argument to pdbxyz it will just ask for a parameter if neither 1) tinker.key file or 2) key file matching coordinate filename, i.e. uncomplexed.key or 3) any key file using the -k argument as in -k my_key.key where any of these 3 options must have the line parameters path/to/amoebabio18.prm.

I'll check some older versions of tinker...

misterbrandonwalker commented 2 years ago

Glad to hear it ;). Can I have example input files for binding? I will try to reproduce.

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From: BJWiley23 @.> Sent: Sunday, May 22, 2022 1:38:14 AM To: TinkerTools/poltype2 @.> Cc: Brandon Walker @.>; Comment @.> Subject: Re: [TinkerTools/poltype2] Experimenting: Psi4 segfault (Issue #11)

Most of my issues with torsion have seem to not be appear after pull last night. However now when running the binding module the first call to pdbxyz uncomplexed.pdb amoebabio18.prm will hang because, maybe it's just newest version of Tinker 8.10.2??, but you cannot input the parameter file as a command line argument to pdbxyz it will just ask for a parameter if neither 1) tinker.key file or 2) key file matching coordinate filename, i.e. uncomplexed.key or 3) any key file using the -k argument as in -k my_key.key where any of these 3 options must have the line parameters path/to/amoebabio18.prm.

Ill let some older version of tinker...

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BJWiley233 commented 2 years ago

Yes here is the other link. It may be more of an issue with the new Tinker programs because pdbxyz will still ask for input parameters even if you give the name of .*prm in the commandline but after I made my own uncomplexed.key file and tested next step calling xyzpdb uncomplexed_comp.xyz amoebabio18.prm accepts the parameter file in the commandline. I'm also using Tinker Version 8.10.2 February 2022.

https://drive.google.com/file/d/126jTKJnqGTJ00LKILVrDyoAyijRf66fK/view?usp=sharing

misterbrandonwalker commented 2 years ago

Fixed now. Essentially pdbxyz needs different input if multiple chains are detected in PDB file. Previously this has only been tested on PDB with one chain.

On Mon, May 23, 2022 at 1:39 PM BJWiley23 @.***> wrote:

Yes here is the other link. It may be more of an issue with the new Tinker programs because pdbxyz will still ask for input parameters even if you give the name of .*prm in the commandline but after I made my own uncomplexed.key file and tested next step calling xyzpdb uncomplexed_comp.xyz amoebabio18.prm accepts the parameter file in the commandline. I'm also using Tinker Version 8.10.2 February 2022.

https://drive.google.com/file/d/126jTKJnqGTJ00LKILVrDyoAyijRf66fK/view?usp=sharing

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BJWiley233 commented 2 years ago

Thanks. Yes I noticed that plus it will also automatically assigned different chains if there is/are missing segments, i.e. this CDK6 structure (5L2T) has missing residues between 48-56, 85-92, and 168-180 and so pdbxyz will output 4 different chains, which I will have to model those in with Modeller before running the simulation. Honestly this is probably a good thing since I was naive to think the PDB was completed. It could be a good idea to try to code this into a warning which will alert the user there are missing residues they need to model else they will have multiple chains. I could do with a pull request unless you are not taking any pull requests.

Not sure if this is why the next step for analyze_gpu uncomplexed_comp.xyz -k final.key is failing with MECHANIC -- Some Required Potential Energy Parameters are Undefined but doesn't sound like it does. Let me know if you get the same error and I will go through the xyz file and params to see what is missing.

misterbrandonwalker commented 2 years ago

So the middle two atom types of the following torsion appear to be incorrect when I examine the output file in pymol. Please let me know if any problems after moddeler is used. I have added a warning if missing atoms are added with pdbxyz.

Torsion 1051-C 1050-CA 1055-C 1056-OH 30 7 7 10

Carboxylate Carbon Methine Carbon Methine Carbon Hydroxyl Oxygen

On Mon, May 23, 2022 at 3:00 PM BJWiley23 @.***> wrote:

Thanks. Yes I noticed that plus it will also automatically assigned different chains if there is/are missing segments, i.e. this CDK6 structure (5L2T) has missing residues between 48-56, 85-92, and 168-180 and so pdbxyz will output 4 different chains, which I will have to model those in with Modeller before running the simulation. Honestly this is probably a good thing since I was naive to think the PDB was completed. It could be a good idea to try to code this into a warning which will alert the user there are missing residues they need to model else they will have multiple chains. I could do with a pull request unless you are not taking any pull requests.

Not sure if this is why the next step for analyze_gpu uncomplexed_comp.xyz -k final.key is failing with MECHANIC -- Some Required Potential Energy Parameters are Undefined but doesn't sound like it does. Let me know if you get the same error and I will go through the xyz file and params to see what is missing.

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BJWiley233 commented 2 years ago

Will do after Modeller! Which file can I view in PyMol? oh you probably mean uncomplexed_comp.pdb

misterbrandonwalker commented 2 years ago

Here is a pymol session with the four atoms saved. I essentially stripped the tinker xyz into cartesian (so some bond information is missing however if you look at connectivity in tinker xyz the torsion is connected).

https://utexas.box.com/s/non3wqi2093i9cwzr6bvule3qjbsldoj

On Mon, May 23, 2022 at 4:01 PM BJWiley23 @.***> wrote:

Will do after Modeller! Which file can I view in PyMol?

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BJWiley233 commented 2 years ago

Wow you are good with PyMol! I would love to know the string of commands to include the torsion or a tutorial 😄 (actually I can probably figure out from side pane). So is the torsion something I can fix using other tools (maybe doing a minimize in Tinker)? Oh wait this is for an UNK residue (wait I'm dumb they are all UNK cause of coortesian).

EDIT: Ah yes so this is for the last residue before the second break in chain (THR 84). So let me run Modeller tonight after work :)

misterbrandonwalker commented 2 years ago

Thank you for your kind words. It looks something like this.

sele atom1051, index 1051 sele atom1050, index 1050 sele atom1055, index 1055 sele atom1056 index 1056

then label, and zoom in pymol gui.

On Mon, May 23, 2022 at 4:09 PM BJWiley23 @.***> wrote:

Wow you are good with PyMol! I would love to know the string of commands to include the torsion or a tutorial 😄

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misterbrandonwalker commented 2 years ago

I have added a wrapped for modeller in poltype see (https://github.com/TinkerTools/poltype2#protein-input-preparation ) it is experimental for the moment and im still learning about all the features but if you'd like, you can try this and see how it works. Feedback would be much appreciated.

BJWiley233 commented 2 years ago

Just looked at the code! Sounds like you learn really quick 😄 (or you've used Modeller before). Looks good so I will test it. Took me like 3 hours to see what I needed to do in Modeller.

misterbrandonwalker commented 2 years ago

It took me over 4 hours but I think this is worth having and common issue. There was some file parsing steps needed to accommodate there missing residue example in there documentation. It is odd to me that they do not provided the file preprocessing as built in functions. It could be that not all the needed information about missing residues is always in crystal PDB, I don’t know how that typically works. There are some different ways to optimize the loop regions or add restraints and I chose their fast refinement option.

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From: BJWiley23 @.> Sent: Tuesday, May 24, 2022 5:00:04 PM To: TinkerTools/poltype2 @.> Cc: Brandon Walker @.>; Comment @.> Subject: Re: [TinkerTools/poltype2] Experimenting: Psi4 segfault (Issue #11)

Just looked at the code! Sounds like you learn really quick 😄 (or you've used Modeller before). Looks good so I will test it. I. Took me like 3 hours to see what I needed to do in Modeller.

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BJWiley233 commented 2 years ago

Yes so the thing is when I tested using the fasta from Uniprot for Q00534 on 5L2T is that one model was definitely way better than the other. The first one the loop literally went through a beta-strand. These where my results using refine.fast and Q00534_fill.BL00020001.pdb was way better. Not sure what molpdf but I wonder if it is an energy so lower is more stable.

>> Summary of successfully produced loop models:
Filename                          molpdf
----------------------------------------
Q00534_fill.BL00010001.pdb     1810.15442
Q00534_fill.BL00020001.pdb      503.69711

See These data would suggest that all of the models are reasonably good, since the scores are close, but TvLDH.B99990001.pdb could be considered the best due to it having both the lowest molpdf and the lowest DOPE score.

misterbrandonwalker commented 2 years ago

Okay great I’ll have to read more about the molpdf score as well

From: BJWiley23 @.> Sent: Tuesday, May 24, 2022 5:13:14 PM To: TinkerTools/poltype2 @.> Cc: Brandon Walker @.>; Comment @.> Subject: Re: [TinkerTools/poltype2] Experimenting: Psi4 segfault (Issue #11)

Yes so the thing is when I tested using the fasta from Uniprot for Q00534 on 5L2T is that one model was definitely way better than the other. The first one the loop literally when through a beta-strand. These where my results using refine.fast and Q00534_fill.BL00020001.pdb was way better. Not sure what molpdf but I wonder if it is an energy so lower is more stable.

Summary of successfully produced loop models: Filename molpdf

Q00534_fill.BL00010001.pdb 1810.15442 Q00534_fill.BL00020001.pdb 503.69711

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BJWiley233 commented 2 years ago

Just as a heads this is kind of silly but deleting ligand atoms from a complexedpdb using openbabel under GenerateUncomplexedProteinPDBFromComplexedPDB somehow screws up some residues in the pdb file that is written to uncomplexedpdb. I have filed an issue here openbabel/openbabel#2481.

Also I tried running the binding model with the input below using an uncomplexedpdb as this seems actually easier for the pipeline, and not sure if this was overlooked but when you do this without including a receptorligandxyzfilename in the poltype.ini file then line 1672 ends up making list where the first value is None type in a list of length 2 and then ComputeBoxSize fails because the first xyzfilename is None.

uncomplexedproteinpdbname=Q00534_fill.BL00020001.fixed.pdb
cpujobsonly=False
numproc=16
binding
ligandxyzfilename=final.xyz
keyfilename=final.key

misterbrandonwalker commented 2 years ago

Good morning,

For the first issue this suggest there may be some issue with the input PDB file. Currently uncomplexedproteinpdbname serves two purposes 1) to determine how many atoms were added by pdbxyz compared to original PDB. Also now its used as inputs for modeller and pdb2pqr for assigning missing residues/protonation states. The function GenerateUncomplexedProteinPDBFromComplexedPDB takes input complexedproteinpdbname as input and keeps anything in file with ATOM, then removes things with HETATM (ligand) to generate the uncomplexedproteinpdbname. I can take a closer look if you provide the PDB. For the second issue, you want to use complexedproteinpdbname, because the ligand needs to be included in the pocket for binding computations.

misterbrandonwalker commented 2 years ago

I would also not worry about "cpujobsonly=False" this is by default false, but I dont include this in docs. Ive used this in very special cases where I wanted to test cpu jobs but my envioronment was set up for GPU jobs. Currently, the program is looking for variable GPUDYNAMICS in the environment then it will switch to tinker 9 (which by my example I call dynamic_gpu, analyze_gpu etc...). Default is CPU tinker for everything. We keep changing tinker9 executable name over time, but if it becomes canonical I can set program to detect canonical executable name instead of searching for GPUDYNAMICS in the environment.

BJWiley233 commented 2 years ago

Here is the uncomplexedproteinpdbname, final.xyz, and final.key in zip folder. https://drive.google.com/file/d/1mGOmRAMToe9MSenqTedMMtDyx3gz1v8E/view?usp=sharing

I tested with the input below:

uncomplexedproteinpdbname=Q00534_fill.BL00020001.fixed.pdb
numproc=16
binding
ligandxyzfilename=final.xyz
keyfilename=final.key

And I get the NoneType error under ComputeBoxSize. My line numbers will be different than yours since I was try to find where the error was occurring but it's this line here.

Traceback (most recent call last):
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 4718, in <module>
    RunPoltype()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 4696, in RunPoltype
    poltype=PolarizableTyper()
  File "<string>", line 332, in __init__
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 1381, in __post_init__
    self.MolecularDynamics()
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/poltype.py", line 2067, in MolecularDynamics
    ann.main(self)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/annihilation.py", line 30, in main
    box.BoxSetupProtocol(poltype)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/boxsetup.py", line 378, in BoxSetupProtocol
    ComputeBoxSize(poltype)
  File "/storage1/fs1/bolton/Active/projects/BWILEYtest/poltype2/PoltypeModules/boxsetup.py", line 23, in ComputeBoxSize
    x,y,z=FindDimensionsOfMoleculeTinkerXYZ(poltype,poltype.outputpath+xyzfilename)
TypeError: can only concatenate str (not "NoneType") to str

misterbrandonwalker commented 2 years ago

So the issue is its expecting complexedproteinpdbname not uncomplexedproteinpdbname. The program needs to be able to know where the ligand is relative to protein. There is a part where in order to get protein xyz file, ligand is removed and then after generating the xyz file the ligand coordinates are added back. Either way though, without the complex wont be able to do binding computations. I would only use uncomplexedproteinpdbname, if you want to use pdb2pqr to add hydrogens, but then you still need to add ligand into the file and give it as complexedproteinpdbname when you want to do binding computations.

BJWiley233 commented 2 years ago

Makes sense. Have you seen any issues where the ligand in the complexed PDB file had incorrect CONECT lines? That I think was the issue for me in that the carbonyl was not represented correctly as double bond in CONECT. I still need to confirm my hypothesis.

misterbrandonwalker commented 2 years ago

I did not check, which program was used to generate the complexed PDB?

On Thu, May 26, 2022 at 3:45 PM BJWiley23 @.***> wrote:

Makes sense. Have you seen any issues where the ligand in the complexed PDB file had incorrect CONECT lines? That I think was the issue for me in that the carbonyl was not represented correctly as double bond in CONECT. I still need to confirm my hypothesis.

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BJWiley233 commented 2 years ago

I naively just added the ligand from original file and it's connections to the output file from Modeller and just ran obabel on it from pdb to pdb. The PDB binding domain did not change much after modelling the loops as shown in the image in the issue I opened under openbabel but also below. I just visually inspected for no contacts but that doesn't mean it's low energy. I haven't been able to test manually making the CONECT a double bond on the oxygen of the ligand.

misterbrandonwalker commented 2 years ago

Great :), I guess I forgot to mention at this step connect records for ligand are not important. The connections in the final.xyz are used as inputs (but coordinates for ligand are still taken from pdb) for making the complexed tinker xyz file.