Explicit valence error when preparing dual topology

[Lumen97]

prepare_dual_topology.py --config_file=step2.ini --output_hidden_temp_dir=false
=============== mdp and run steps=================
         Complex                    Water          
        min01.mdp                 min01.mdp        
        min02.mdp                 min02.mdp        
        min03.mdp                  nve.mdp         
         nve.mdp                   nvt.mdp         
         nvt.mdp                   npt.mdp         
         npt.mdp                   md.mdp          
         md.mdp                       -            
==================================================
================= Input ligands ==================
   Name         Molecule            Topology      
  drg_1    [H]C#Cc1c(F)c([H])c([H])c2c([H])c(O[H])c([H])c(-c3nc([H])c4c(N5C([H])([H])C6([H])C([H])([H])C([H])([H])C([H])(C5([H])[H])[N+]6([H])[H])nc(OC([H])([H])C56C([H])([H])C([H])([H])C([H])([H])[N+]5([H])C([H])([H])C([H])(F)C6([H])[H])nc4c3Cl)c12 lig_data/drg_1.itp 
  drg_2    [H]C#Cc1c(Cl)c([H])c([H])c2c([H])c(O[H])c([H])c(-c3nc([H])c4c(N5C([H])([H])C6([H])C([H])([H])C([H])([H])C([H])(C5([H])[H])[N+]6([H])[H])nc(OC([H])([H])C56C([H])([H])C([H])([H])C([H])([H])[N+]5([H])C([H])([H])C([H])(F)C6([H])[H])nc4c3F)c12 lig_data/drg_2.itp 
  drg_3    [H]C#Cc1c(F)c([H])c([H])c2c([H])c([H])c([H])c(-c3nc([H])c4c(N5C([H])([H])C6([H])C([H])([H])C([H])([H])C([H])(C5([H])[H])[N+]6([H])[H])nc(OC([H])([H])C56C([H])([H])C([H])([H])C([H])([H])[N+]5([H])C([H])([H])C([H])(F)C6([H])[H])nc4c3F)c12 lig_data/drg_3.itp 
==================================================
=================== Poses read ===================
Name            File                 Details             
drg_1           {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x7f52b40520d8>, 'topology': ['lig_data/drg_1.itp']}                   
drg_2           {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x7f52b4052298>, 'topology': ['lig_data/drg_2.itp']}                   
drg_3           {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x7f52b4052110>, 'topology': ['lig_data/drg_3.itp']}                   
=============== Superimposed poses ===============
Name            File                      Note           
Traceback (most recent call last):
  File "/home/cadd/program/fep/prepare_dual_topology.py", line 3451, in <module>
    verbosity=arguments.verbose, **arguments.poses_advanced_options)
  File "/home/cadd/program/fep/prepare_dual_topology.py", line 2878, in align_ligands
    save_state=save_state, verbosity=verbosity, **kwargs)
  File "/home/cadd/program/fep/docking_readers/superimpose_loader.py", line 127, in superimpose_poses
    atom_map=this_atommap, **kwargs)
  File "/home/cadd/program/fep/os_util.py", line 517, in wrap_trace
    return f(*args, **kwargs)
  File "/home/cadd/program/fep/merge_topologies.py", line 243, in constrained_embed_shapeselect
    core_mol = rdkit.Chem.RemoveHs(core_mol)
rdkit.Chem.rdchem.MolSanitizeException: Explicit valence for atom # 7 C, 5, is greater than permitted

workdir.zip

---

2022-07-12: formatting (@luancarvalhomartins)

[luancarvalhomartins]

Thank you for your message and for your interest in PyAutoFEP.

You are using a quite complex molecule as the reference pose for the superimpose (receptor_data/1.pdb), but passing it in PDB format. You should (a) pass it using another (eg, .mol or .mol2) format or (b) adding a SMILES to your PDB file:

REMARK SMILES Oc1cc(-c2ncc3c(nc(OC[C@@]45CCC[N@@H+]4C[C@H](F)C5)nc3c2F)N2C[C@@H]3CC[C@H](C2)[NH2+]3)c2c(C#C)c(F)ccc2c1

By adding that to the first line of your 1.pdb (1.tar.gz) file I was able to prepare the perturbations using your inputs. I also had to run rename_res.sh in your receptor_data/receptor.pdb. Please, find attached the output file I generated (20220712_lumen97_data.tar.gz).

[Lumen97]

thank you for your reply。

The same error happens during the "Run FEP" step. https://github.com/luancarvalhomartins/PyAutoFEP/issues/52#issue-1267165606

If I use the gmx_mpi version of Gromacs

$ prepare_dual_topology.py --config_file=step2.ini --output_hidden_temp_dir=false
...........................................
================ Working on pairs ================
Perturbation Pose Coordinates
============= Working on drg_1-drg_2 =============
drg_1 -> drg_2
================ Building system =================
Traceback (most recent call last):
  File "/home/cadd/program/fep/prepare_dual_topology.py", line 3770, in <module>
    verbosity=arguments.verbose)
  File "/home/cadd/program/fep/os_util.py", line 529, in wrap_trace
    return f(*args, **kwargs)
  File "/home/cadd/program/fep/prepare_dual_topology.py", line 283, in prepare_complex_system
    os_util.run_gmx(gmx_bin, pdb2gmx_list, communicate_str, build_files_dict['pdb2gmx_log'], verbosity=verbosity)
  File "/home/cadd/program/fep/os_util.py", line 149, in run_gmx
    stdin=subprocess.PIPE, universal_newlines=True, env=this_env, cwd=cwd)
  File "/home/cadd/program/conda/envs/fep/lib/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/home/cadd/program/conda/envs/fep/lib/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'gmx': 'gmx'

"Run FEP" step，If I use the gmx or gmx_mpi version of Gromacs

tar: */water/md/rerun/*.pkl: Cannot stat: No such file or directory
tar: */water/md/rerun/*.xvg: Cannot stat: No such file or directory
tar: */water/md/rerun/*.edr: Cannot stat: No such file or directory
tar: */protein/md/rerun/*.pkl: Cannot stat: No such file or directory
tar: */protein/md/rerun/*.xvg: Cannot stat: No such file or directory
tar: */protein/md/rerun/*.edr: Cannot stat: No such file or directory
tar: */water/md/lambda*/lambda_pbcfit.xtc: Cannot stat: No such file or directory
tar: */water/md/lambda*/lambda.log: Cannot stat: No such file or directory
tar: */water/md/lambda*/lambda.edr: Cannot stat: No such file or directory
tar: */protein/md/lambda*/lambda_pbcfit.xtc: Cannot stat: No such file or directory
tar: */protein/md/lambda*/lambda.log: Cannot stat: No such file or directory
tar: */protein/md/lambda*/lambda.edr: Cannot stat: No such file or directory
tar: */water/md/lambda*/analysis.log: Cannot stat: No such file or directory
tar: */protein/md/lambda*/analysis.log: Cannot stat: No such file or directory
tar: */water/md/analysis/*.xvg: Cannot stat: No such file or directory
tar: */protein/md/analysis/*.xvg: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors

I'm not really sure if the step2.ini file is correct

and bashrc

workdir.zip

---

2022-07-13: formatting (@luancarvalhomartins)

[luancarvalhomartins]

The step2.ini file must suit your install paths. The executable passed to gmx_bin_run will be executed in the minimize, equilibrate, run, rerun, and analyze steps. Therefore, in your case, PyAutoFEP run script will run /usr/local/gromacs/bin/GMXRC. Make sure gmx_bin_run points to a valid, MPI-compatible GROMACS executable in the run node.

[Lumen97]

As shown in the diagram，I used the MPI-compatible GROMACS (2021.5)，gmx_bin_run = gmx_mpi (/home/cadd/program/gromacs/bin/GMXRC), but in the prepare_dual_topology step, it reported “No such file or directory: 'gmx': 'gmx'”

MPI-incompatible GROMACS (/usr/local/gromacs/bin/GMXRC), gmx_bin_run = gmx, it reported tar: /water/md/rerun/.pkl: Cannot stat: No such file or directory tar: /water/md/rerun/.xvg: Cannot stat: No such file or directory...............

I'm sorry for my poor English, hope you can understand my meaning.

[luancarvalhomartins]

By passing gmx_bin_run = gmx_mpi, you are telling the run script to use gmx_mpi. prepare_dual_topology.py, on the other hand, uses the executable in gmx_bin_local to run editconf, solvate etc. From prepare_dual_topology.py --help:

  --gmx_bin_local GMX_BIN_LOCAL
                        Use this local Gromacs binary to prepare the system
                        (Default: gmx)
  --gmx_bin_run GMX_BIN_RUN
                        Use this Gromacs binary to run the MD. This should be
                        the Gromacs bin in the run node,not in the current
                        machine. (Default: gmx_mpi)

Make sure you have a GROMACS build in the machine you are running prepare_dual_topology.py and that gmx_bin_local points to a executable, either gmx or gmx_mpi should work. Make sure you have a MPI-compatible GROMACS build in you run machine and that gmx_bin_run points to a gmx_mpi executable.

[Lumen97]

Thanks a lot, but I got this error message:

rerun folder is empty，drg*-drg*/protein/md/feprun.log feprun_130610_14072022.log

drg*-drg/protein/lambda/md/md.log mdout_nocont.log mdout.log

[luancarvalhomartins]

You got a segfault. There is something wrong with MPI or gmx_mpi. Please, test your MPI-compatible GROMACS installation (ie, gmx_mpi), make sure it runs using -multidir.

[Lumen97]

Thanks for your suggestion. I rebuilt openmpi and gromacs, but after running for a few hours, the tar error appeared again，and there seem to be no errors in the feprun.log file。

feprun_145223_15072022.log lambda.log mdout.log

[luancarvalhomartins]

There are no errors in the outputs you attached, and it seems the MD finished correctly. What is the error message you see? Did the MD really run?

[Lumen97]

Yes，the MD really ran and generated a total of 21.2gb of files，but the rerun folder is empty, tar errors appeared about 6 hours after "bash run all"

[Lumen97]

drg_1-drg_2/runall_drg_1-drg_2_protein.sh: line368: Syntax error near unexpected token ')'
drg_1-drg_2/runall_drg_1-drg_2_protein.sh: line 368: `if [ $(ls lambda*/lambda_pbcfit.xtc 2>/dev/null | wc -l) -ne ${n_lambda} **)**'
drg_1-drg_3/runall_drg_3-drg_1_protein.sh: line368: Syntax error near unexpected token ')'

I changed it to ]，and then

............................................................................................
GROMACS:      gmx energy, version 2021.5
Executable:   /home/cadd/program/gromacs-mpi/bin/gmx_mpi
Data prefix:  /home/cadd/program/gromacs-mpi
Working dir:  /media/cadd/1857f441-374b-4242-a78d-007ca5df83ce/data/fep/perturbations1/drg_1-drg_3/protein/md/rerun
Command line:
  gmx_mpi energy -f rerun_struct9_coord9.edr -o rerun_struct9_coord9.xvg

Opened rerun_struct9_coord9.edr as single precision energy file

Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.

  1  Bond             2  Angle            3  Ryckaert-Bell.   4  Improper-Dih. 
  5  LJ-14            6  Coulomb-14       7  LJ-(SR)          8  Disper.-corr. 
  9  Coulomb-(SR)    10  Coul.-recip.    11  Potential       12  Box-X         
 13  Box-Y           14  Box-Z           15  Volume          16  Density       

Last energy frame read 2500 time 5000.000         

GROMACS reminds you: "Don't Follow Me Home" (Throwing Muses)

environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
environment: rerun/rerun_struct_coord.out: No such file or directory
tar: */water/md/lambda*/analysis.log: Cannot stat: No such file or directory
tar: */protein/md/lambda*/analysis.log: Cannot stat: No such file or directory
tar: */water/md/analysis/*.xvg: Cannot stat: No such file or directory
tar: */protein/md/analysis/*.xvg: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors

runall_drg_1-drg_2_protein.zip rerun_joblog_110559_19072022.log rerun_struct9_coord9.log

protein/md/lambda*/ ls analysis.log lambda.cpt lambda.edr lambda.gro lambda.log lambda_nocont.tpr lambda_prev.cpt lambda.tpr lambda.trr plumed.dat

I found that the lambda.trr file exists，and lambda_pbcfit.xtc was missing, What could be the cause of this？

lambda.log analysis.log

[luancarvalhomartins]

Thanks for letting me know about the ) typo. Fixed it.

It seems the PBC code did not run. Would you mind retrying after replacing the lines from 368 to the end of fi with following lines in drg_1-drg_2/runall_drg_1-drg_2_protein.sh? (I added made that change in the last commit, but because you already ran everything it will be much easier just update the run script)

Replace this:

           if [ $(ls lambda*/lambda_pbcfit.xtc 2>/dev/null | wc -l) -ne ${n_lambda} )
           then
               parallel --jobs=1 --joblog analysis_joblog_$(date "+%H%M%S_%d%m%Y").log 'cd {//} && [ ! -f "{.}_pbcfit.xtc" ] && fn' ::: ${trajectory_files}
           fi

With this:

           trajectory_files=$(ls -v lambda*/lambda.tpr)
           parallel --jobs=1 --joblog analysis_joblog_$(date "+%H%M%S_%d%m%Y").log --env fn --env pbc_cluster 'cd {//} && [ ! -f "lambda_pbcfit.xtc" ] && fn' ::: ${trajectory_files}

Just to be sure, did you get the unk_matrix.pkl file in rerun/? lambda_pbcfit.xtcis used for further analysis, but should not interfere with the ddG estimative.

[Lumen97]

Hi. I still encountered environment: rerun/rerun_struct_coord.out: No such file or directory errors. My perturbation_dir is /program/fep/workdir/fep, and I get the unk_matrix.pkl file in rerun/ unk_matrix.zip

cadd@huiyu:~/program/fep/workdir/fep/drg_1-drg_2/protein/md/rerun$ ls

lambda0.xvg rerun_struct11_coord8.edr rerun_struct3_coord9.edr rerun_struct7_coord0.edr lambda10.xvg rerun_struct11_coord8.log rerun_struct3_coord9.log rerun_struct7_coord0.log lambda11.xvg rerun_struct11_coord8.out rerun_struct3_coord9.out rerun_struct7_coord0.out lambda1.xvg rerun_struct11_coord8.xvg rerun_struct3_coord9.xvg rerun_struct7_coord0.xvg lambda2.xvg rerun_struct11_coord9.edr rerun_struct4_coord0.edr rerun_struct7_coord10.edr lambda3.xvg rerun_struct11_coord9.log rerun_struct4_coord0.log rerun_struct7_coord10.log lambda4.xvg rerun_struct11_coord9.out rerun_struct4_coord0.out rerun_struct7_coord10.out lambda5.xvg rerun_struct11_coord9.xvg rerun_struct4_coord0.xvg rerun_struct7_coord10.xvg lambda6.xvg rerun_struct1_coord0.edr rerun_struct4_coord10.edr rerun_struct7_coord11.edr lambda7.xvg rerun_struct1_coord0.log rerun_struct4_coord10.log rerun_struct7_coord11.log lambda8.xvg rerun_struct1_coord0.out rerun_struct4_coord10.out rerun_struct7_coord11.out lambda9.xvg rerun_struct1_coord0.xvg rerun_struct4_coord10.xvg rerun_struct7_coord11.xvg rerun_struct0_coord0.edr rerun_struct1_coord10.edr rerun_struct4_coord11.edr rerun_struct7_coord1.edr rerun_struct0_coord0.log rerun_struct1_coord10.log rerun_struct4_coord11.log rerun_struct7_coord1.log rerun_struct0_coord0.out rerun_struct1_coord10.out rerun_struct4_coord11.out rerun_struct7_coord1.out rerun_struct0_coord0.xvg rerun_struct1_coord10.xvg rerun_struct4_coord11.xvg rerun_struct7_coord1.xvg rerun_struct0_coord10.edr rerun_struct1_coord11.edr rerun_struct4_coord1.edr rerun_struct7_coord2.edr rerun_struct0_coord10.log rerun_struct1_coord11.log rerun_struct4_coord1.log rerun_struct7_coord2.log rerun_struct0_coord10.out rerun_struct1_coord11.out rerun_struct4_coord1.out rerun_struct7_coord2.out rerun_struct0_coord10.xvg rerun_struct1_coord11.xvg rerun_struct4_coord1.xvg rerun_struct7_coord2.xvg rerun_struct0_coord11.edr rerun_struct1_coord1.edr rerun_struct4_coord2.edr rerun_struct7_coord3.edr rerun_struct0_coord11.log rerun_struct1_coord1.log rerun_struct4_coord2.log rerun_struct7_coord3.log rerun_struct0_coord11.out rerun_struct1_coord1.out rerun_struct4_coord2.out rerun_struct7_coord3.out rerun_struct0_coord11.xvg rerun_struct1_coord1.xvg rerun_struct4_coord2.xvg rerun_struct7_coord3.xvg rerun_struct0_coord1.edr rerun_struct1_coord2.edr rerun_struct4_coord3.edr rerun_struct7_coord4.edr rerun_struct0_coord1.log rerun_struct1_coord2.log rerun_struct4_coord3.log rerun_struct7_coord4.log rerun_struct0_coord1.out rerun_struct1_coord2.out rerun_struct4_coord3.out rerun_struct7_coord4.out rerun_struct0_coord1.xvg rerun_struct1_coord2.xvg rerun_struct4_coord3.xvg rerun_struct7_coord4.xvg rerun_struct0_coord2.edr rerun_struct1_coord3.edr rerun_struct4_coord4.edr rerun_struct7_coord5.edr rerun_struct0_coord2.log rerun_struct1_coord3.log rerun_struct4_coord4.log rerun_struct7_coord5.log rerun_struct0_coord2.out rerun_struct1_coord3.out rerun_struct4_coord4.out rerun_struct7_coord5.out rerun_struct0_coord2.xvg rerun_struct1_coord3.xvg rerun_struct4_coord4.xvg rerun_struct7_coord5.xvg rerun_struct0_coord3.edr rerun_struct1_coord4.edr rerun_struct4_coord5.edr rerun_struct7_coord6.edr rerun_struct0_coord3.log rerun_struct1_coord4.log rerun_struct4_coord5.log rerun_struct7_coord6.log rerun_struct0_coord3.out rerun_struct1_coord4.out rerun_struct4_coord5.out rerun_struct7_coord6.out rerun_struct0_coord3.xvg rerun_struct1_coord4.xvg rerun_struct4_coord5.xvg rerun_struct7_coord6.xvg rerun_struct0_coord4.edr rerun_struct1_coord5.edr rerun_struct4_coord6.edr rerun_struct7_coord7.edr rerun_struct0_coord4.log rerun_struct1_coord5.log rerun_struct4_coord6.log rerun_struct7_coord7.log rerun_struct0_coord4.out rerun_struct1_coord5.out rerun_struct4_coord6.out rerun_struct7_coord7.out rerun_struct0_coord4.xvg rerun_struct1_coord5.xvg rerun_struct4_coord6.xvg rerun_struct7_coord7.xvg rerun_struct0_coord5.edr rerun_struct1_coord6.edr rerun_struct4_coord7.edr rerun_struct7_coord8.edr rerun_struct0_coord5.log rerun_struct1_coord6.log rerun_struct4_coord7.log rerun_struct7_coord8.log rerun_struct0_coord5.out rerun_struct1_coord6.out rerun_struct4_coord7.out rerun_struct7_coord8.out rerun_struct0_coord5.xvg rerun_struct1_coord6.xvg rerun_struct4_coord7.xvg rerun_struct7_coord8.xvg rerun_struct0_coord6.edr rerun_struct1_coord7.edr rerun_struct4_coord8.edr rerun_struct7_coord9.edr rerun_struct0_coord6.log rerun_struct1_coord7.log rerun_struct4_coord8.log rerun_struct7_coord9.log rerun_struct0_coord6.out rerun_struct1_coord7.out rerun_struct4_coord8.out rerun_struct7_coord9.out rerun_struct0_coord6.xvg rerun_struct1_coord7.xvg rerun_struct4_coord8.xvg rerun_struct7_coord9.xvg rerun_struct0_coord7.edr rerun_struct1_coord8.edr rerun_struct4_coord9.edr rerun_struct8_coord0.edr rerun_struct0_coord7.log rerun_struct1_coord8.log rerun_struct4_coord9.log rerun_struct8_coord0.log rerun_struct0_coord7.out rerun_struct1_coord8.out rerun_struct4_coord9.out rerun_struct8_coord0.out rerun_struct0_coord7.xvg rerun_struct1_coord8.xvg rerun_struct4_coord9.xvg rerun_struct8_coord0.xvg rerun_struct0_coord8.edr rerun_struct1_coord9.edr rerun_struct5_coord0.edr rerun_struct8_coord10.edr rerun_struct0_coord8.log rerun_struct1_coord9.log rerun_struct5_coord0.log rerun_struct8_coord10.log rerun_struct0_coord8.out rerun_struct1_coord9.out rerun_struct5_coord0.out rerun_struct8_coord10.out rerun_struct0_coord8.xvg rerun_struct1_coord9.xvg rerun_struct5_coord0.xvg rerun_struct8_coord10.xvg rerun_struct0_coord9.edr rerun_struct2_coord0.edr rerun_struct5_coord10.edr rerun_struct8_coord11.edr rerun_struct0_coord9.log rerun_struct2_coord0.log rerun_struct5_coord10.log rerun_struct8_coord11.log rerun_struct0_coord9.out rerun_struct2_coord0.out rerun_struct5_coord10.out rerun_struct8_coord11.out rerun_struct0_coord9.xvg rerun_struct2_coord0.xvg rerun_struct5_coord10.xvg rerun_struct8_coord11.xvg rerun_struct10_coord0.edr rerun_struct2_coord10.edr rerun_struct5_coord11.edr rerun_struct8_coord1.edr rerun_struct10_coord0.log rerun_struct2_coord10.log rerun_struct5_coord11.log rerun_struct8_coord1.log rerun_struct10_coord0.out rerun_struct2_coord10.out rerun_struct5_coord11.out rerun_struct8_coord1.out rerun_struct10_coord0.xvg rerun_struct2_coord10.xvg rerun_struct5_coord11.xvg rerun_struct8_coord1.xvg rerun_struct10_coord10.edr rerun_struct2_coord11.edr rerun_struct5_coord1.edr rerun_struct8_coord2.edr rerun_struct10_coord10.log rerun_struct2_coord11.log rerun_struct5_coord1.log rerun_struct8_coord2.log rerun_struct10_coord10.out rerun_struct2_coord11.out rerun_struct5_coord1.out rerun_struct8_coord2.out rerun_struct10_coord10.xvg rerun_struct2_coord11.xvg rerun_struct5_coord1.xvg rerun_struct8_coord2.xvg rerun_struct10_coord11.edr rerun_struct2_coord1.edr rerun_struct5_coord2.edr rerun_struct8_coord3.edr rerun_struct10_coord11.log rerun_struct2_coord1.log rerun_struct5_coord2.log rerun_struct8_coord3.log rerun_struct10_coord11.out rerun_struct2_coord1.out rerun_struct5_coord2.out rerun_struct8_coord3.out rerun_struct10_coord11.xvg rerun_struct2_coord1.xvg rerun_struct5_coord2.xvg rerun_struct8_coord3.xvg rerun_struct10_coord1.edr rerun_struct2_coord2.edr rerun_struct5_coord3.edr rerun_struct8_coord4.edr rerun_struct10_coord1.log rerun_struct2_coord2.log rerun_struct5_coord3.log rerun_struct8_coord4.log rerun_struct10_coord1.out rerun_struct2_coord2.out rerun_struct5_coord3.out rerun_struct8_coord4.out rerun_struct10_coord1.xvg rerun_struct2_coord2.xvg rerun_struct5_coord3.xvg rerun_struct8_coord4.xvg rerun_struct10_coord2.edr rerun_struct2_coord3.edr rerun_struct5_coord4.edr rerun_struct8_coord5.edr rerun_struct10_coord2.log rerun_struct2_coord3.log rerun_struct5_coord4.log rerun_struct8_coord5.log rerun_struct10_coord2.out rerun_struct2_coord3.out rerun_struct5_coord4.out rerun_struct8_coord5.out rerun_struct10_coord2.xvg rerun_struct2_coord3.xvg rerun_struct5_coord4.xvg rerun_struct8_coord5.xvg rerun_struct10_coord3.edr rerun_struct2_coord4.edr rerun_struct5_coord5.edr rerun_struct8_coord6.edr rerun_struct10_coord3.log rerun_struct2_coord4.log rerun_struct5_coord5.log rerun_struct8_coord6.log rerun_struct10_coord3.out rerun_struct2_coord4.out rerun_struct5_coord5.out rerun_struct8_coord6.out rerun_struct10_coord3.xvg rerun_struct2_coord4.xvg rerun_struct5_coord5.xvg rerun_struct8_coord6.xvg rerun_struct10_coord4.edr rerun_struct2_coord5.edr rerun_struct5_coord6.edr rerun_struct8_coord7.edr rerun_struct10_coord4.log rerun_struct2_coord5.log rerun_struct5_coord6.log rerun_struct8_coord7.log rerun_struct10_coord4.out rerun_struct2_coord5.out rerun_struct5_coord6.out rerun_struct8_coord7.out rerun_struct10_coord4.xvg rerun_struct2_coord5.xvg rerun_struct5_coord6.xvg rerun_struct8_coord7.xvg rerun_struct10_coord5.edr rerun_struct2_coord6.edr rerun_struct5_coord7.edr rerun_struct8_coord8.edr rerun_struct10_coord5.log rerun_struct2_coord6.log rerun_struct5_coord7.log rerun_struct8_coord8.log rerun_struct10_coord5.out rerun_struct2_coord6.out rerun_struct5_coord7.out rerun_struct8_coord8.out rerun_struct10_coord5.xvg rerun_struct2_coord6.xvg rerun_struct5_coord7.xvg rerun_struct8_coord8.xvg rerun_struct10_coord6.edr rerun_struct2_coord7.edr rerun_struct5_coord8.edr rerun_struct8_coord9.edr rerun_struct10_coord6.log rerun_struct2_coord7.log rerun_struct5_coord8.log rerun_struct8_coord9.log rerun_struct10_coord6.out rerun_struct2_coord7.out rerun_struct5_coord8.out rerun_struct8_coord9.out rerun_struct10_coord6.xvg rerun_struct2_coord7.xvg rerun_struct5_coord8.xvg rerun_struct8_coord9.xvg rerun_struct10_coord7.edr rerun_struct2_coord8.edr rerun_struct5_coord9.edr rerun_struct9_coord0.edr rerun_struct10_coord7.log rerun_struct2_coord8.log rerun_struct5_coord9.log rerun_struct9_coord0.log rerun_struct10_coord7.out rerun_struct2_coord8.out rerun_struct5_coord9.out rerun_struct9_coord0.out rerun_struct10_coord7.xvg rerun_struct2_coord8.xvg rerun_struct5_coord9.xvg rerun_struct9_coord0.xvg rerun_struct10_coord8.edr rerun_struct2_coord9.edr rerun_struct6_coord0.edr rerun_struct9_coord10.edr rerun_struct10_coord8.log rerun_struct2_coord9.log rerun_struct6_coord0.log rerun_struct9_coord10.log rerun_struct10_coord8.out rerun_struct2_coord9.out rerun_struct6_coord0.out rerun_struct9_coord10.out rerun_struct10_coord8.xvg rerun_struct2_coord9.xvg rerun_struct6_coord0.xvg rerun_struct9_coord10.xvg rerun_struct10_coord9.edr rerun_struct3_coord0.edr rerun_struct6_coord10.edr rerun_struct9_coord11.edr rerun_struct10_coord9.log rerun_struct3_coord0.log rerun_struct6_coord10.log rerun_struct9_coord11.log rerun_struct10_coord9.out rerun_struct3_coord0.out rerun_struct6_coord10.out rerun_struct9_coord11.out rerun_struct10_coord9.xvg rerun_struct3_coord0.xvg rerun_struct6_coord10.xvg rerun_struct9_coord11.xvg rerun_struct11_coord0.edr rerun_struct3_coord10.edr rerun_struct6_coord11.edr rerun_struct9_coord1.edr rerun_struct11_coord0.log rerun_struct3_coord10.log rerun_struct6_coord11.log rerun_struct9_coord1.log rerun_struct11_coord0.out rerun_struct3_coord10.out rerun_struct6_coord11.out rerun_struct9_coord1.out rerun_struct11_coord0.xvg rerun_struct3_coord10.xvg rerun_struct6_coord11.xvg rerun_struct9_coord1.xvg rerun_struct11_coord10.edr rerun_struct3_coord11.edr rerun_struct6_coord1.edr rerun_struct9_coord2.edr rerun_struct11_coord10.log rerun_struct3_coord11.log rerun_struct6_coord1.log rerun_struct9_coord2.log rerun_struct11_coord10.out rerun_struct3_coord11.out rerun_struct6_coord1.out rerun_struct9_coord2.out rerun_struct11_coord10.xvg rerun_struct3_coord11.xvg rerun_struct6_coord1.xvg rerun_struct9_coord2.xvg rerun_struct11_coord11.edr rerun_struct3_coord1.edr rerun_struct6_coord2.edr rerun_struct9_coord3.edr rerun_struct11_coord11.log rerun_struct3_coord1.log rerun_struct6_coord2.log rerun_struct9_coord3.log rerun_struct11_coord11.out rerun_struct3_coord1.out rerun_struct6_coord2.out rerun_struct9_coord3.out rerun_struct11_coord11.xvg rerun_struct3_coord1.xvg rerun_struct6_coord2.xvg rerun_struct9_coord3.xvg rerun_struct11_coord1.edr rerun_struct3_coord2.edr rerun_struct6_coord3.edr rerun_struct9_coord4.edr rerun_struct11_coord1.log rerun_struct3_coord2.log rerun_struct6_coord3.log rerun_struct9_coord4.log rerun_struct11_coord1.out rerun_struct3_coord2.out rerun_struct6_coord3.out rerun_struct9_coord4.out rerun_struct11_coord1.xvg rerun_struct3_coord2.xvg rerun_struct6_coord3.xvg rerun_struct9_coord4.xvg rerun_struct11_coord2.edr rerun_struct3_coord3.edr rerun_struct6_coord4.edr rerun_struct9_coord5.edr rerun_struct11_coord2.log rerun_struct3_coord3.log rerun_struct6_coord4.log rerun_struct9_coord5.log rerun_struct11_coord2.out rerun_struct3_coord3.out rerun_struct6_coord4.out rerun_struct9_coord5.out rerun_struct11_coord2.xvg rerun_struct3_coord3.xvg rerun_struct6_coord4.xvg rerun_struct9_coord5.xvg rerun_struct11_coord3.edr rerun_struct3_coord4.edr rerun_struct6_coord5.edr rerun_struct9_coord6.edr rerun_struct11_coord3.log rerun_struct3_coord4.log rerun_struct6_coord5.log rerun_struct9_coord6.log rerun_struct11_coord3.out rerun_struct3_coord4.out rerun_struct6_coord5.out rerun_struct9_coord6.out rerun_struct11_coord3.xvg rerun_struct3_coord4.xvg rerun_struct6_coord5.xvg rerun_struct9_coord6.xvg rerun_struct11_coord4.edr rerun_struct3_coord5.edr rerun_struct6_coord6.edr rerun_struct9_coord7.edr rerun_struct11_coord4.log rerun_struct3_coord5.log rerun_struct6_coord6.log rerun_struct9_coord7.log rerun_struct11_coord4.out rerun_struct3_coord5.out rerun_struct6_coord6.out rerun_struct9_coord7.out rerun_struct11_coord4.xvg rerun_struct3_coord5.xvg rerun_struct6_coord6.xvg rerun_struct9_coord7.xvg rerun_struct11_coord5.edr rerun_struct3_coord6.edr rerun_struct6_coord7.edr rerun_struct9_coord8.edr rerun_struct11_coord5.log rerun_struct3_coord6.log rerun_struct6_coord7.log rerun_struct9_coord8.log rerun_struct11_coord5.out rerun_struct3_coord6.out rerun_struct6_coord7.out rerun_struct9_coord8.out rerun_struct11_coord5.xvg rerun_struct3_coord6.xvg rerun_struct6_coord7.xvg rerun_struct9_coord8.xvg rerun_struct11_coord6.edr rerun_struct3_coord7.edr rerun_struct6_coord8.edr rerun_struct9_coord9.edr rerun_struct11_coord6.log rerun_struct3_coord7.log rerun_struct6_coord8.log rerun_struct9_coord9.log rerun_struct11_coord6.out rerun_struct3_coord7.out rerun_struct6_coord8.out rerun_struct9_coord9.out rerun_struct11_coord6.xvg rerun_struct3_coord7.xvg rerun_struct6_coord8.xvg rerun_struct9_coord9.xvg rerun_struct11_coord7.edr rerun_struct3_coord8.edr rerun_struct6_coord9.edr unk_matrix.pkl rerun_struct11_coord7.log rerun_struct3_coord8.log rerun_struct6_coord9.log rerun_struct11_coord7.out rerun_struct3_coord8.out rerun_struct6_coord9.out rerun_struct11_coord7.xvg rerun_struct3_coord8.xvg rerun_struct6_coord9.xvg

(fep) cadd@huiyu:~/program/fep/workdir/fep$ bash runall.sh

environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory environment: rerun/rerun_struct_coord.out: No such file or directory tar: /water/md/lambda/analysis.log: Cannot stat: No such file or directory tar: /protein/md/lambda/analysis.log: Cannot stat: No such file or directory tar: /water/md/analysis/.xvg: Cannot stat: No such file or directory tar: /protein/md/analysis/.xvg: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors

[luancarvalhomartins]

Sorry for the tardiness. I have been super swamped these days.

That's quite strange. All .xvg files are there and the script should not test for the .out files. I will take a look when possible.

PS: I am also filling a separeted issue.