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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. #1074

Closed H-EKE closed 10 months ago

H-EKE commented 10 months ago

Hi,

I am trying to build a protein-ligand system with HTMD. The input file is a pdb.

I parametrized the ligand with charmgui-web server, but I don't understand why I am getting the following log error.

psfgen) building segment H
psfgen) reading residues from pdb file segments/segmentH.pdb
psfgen) extracted 1 residues from pdb file
psfgen) Info: generating structure...psfgen) unknown atom type SG2P1
psfgen) add atom failed in residue GSP:413
failed!
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
    while executing
"segment H {
        pdb segments/segmentH.pdb
}"
    (file "./build.vmd" line 178)

MY param file for the ligand


* Parameters generated by analogy by
* CHARMM General Force Field (CGenFF) program version 2.5.1
*

! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

BONDS
CG3C53 NG2R52  320.00     1.4600 ! GSP , from CG3C54 NG2R52, penalty= 4

ANGLES
CG3C51 CG3C53 NG2R52   68.00    106.00 ! GSP , from CG3C54 CG3C54 NG2R52, penalty= 28.4
NG2R52 CG3C53 OG3C51  140.00    108.00 ! GSP , from NG2R51 CG3C51 OG3C51, penalty= 34
NG2R52 CG3C53 HGA1     54.00    107.00 ! GSP , from NG2R52 CG3C54 HGA2, penalty= 4
CG2R53 NG2R52 CG3C53  140.00    108.00 ! GSP , from CG2R53 NG2R52 CG3C54, penalty= 0.4
CG2RC0 NG2R52 CG3C53  101.00    111.90 ! GSP , from CG2R52 NG2R52 CG3C54, penalty= 3.4
PG0    OG304  PG1      45.00    143.00   40.00   3.25000 ! GSP , from PG0 OG304 PG0, penalty= 2

DIHEDRALS
NG2R52 CG2R53 NG2R52 CG3C53     7.7000  2   180.00 ! GSP , from NG2R52 CG2R53 NG2R52 CG3C54, penalty= 0.4
HGR53  CG2R53 NG2R52 CG3C53     6.3000  2   180.00 ! GSP , from HGR53 CG2R53 NG2R52 CG3C54, penalty= 0.4
CG2R63 CG2RC0 NG2R52 HGP2       1.6000  2   180.00 ! GSP , from CG2RC0 CG2RC0 NG2R52 HGP2, penalty= 47.5
CG2RC0 CG2RC0 NG2R52 CG3C53     5.5000  2   180.00 ! GSP , from CG2RC0 CG2RC0 NG2R52 CG334, penalty= 28.2
NG2R62 CG2RC0 NG2R52 CG3C53     3.0000  2   180.00 ! GSP , from NG2R62 CG2RC0 NG2R52 CG334, penalty= 28.2
CG3C51 CG3C51 CG3C53 NG2R52     0.0000  3     0.00 ! GSP , from CG3C51 CG3C51 CG3C51 NG2R51, penalty= 34
OG311  CG3C51 CG3C53 NG2R52     0.0000  3     0.00 ! GSP , from NG2R51 CG3C51 CG3C51 OG311, penalty= 34
HGA1   CG3C51 CG3C53 NG2R52     0.3000  3     0.00 ! GSP , from NG2R52 CG3C54 CG3C54 HGA2, penalty= 9
CG3C51 CG3C53 NG2R52 CG2R53     0.2500  3   180.00 ! GSP , from CG3C54 CG3C54 NG2R52 CG2R53, penalty= 28.4
CG3C51 CG3C53 NG2R52 CG2RC0     0.2500  3   180.00 ! GSP , from CG3C54 CG3C54 NG2R52 CG2R53, penalty= 32.4
OG3C51 CG3C53 NG2R52 CG2R53     0.2500  3   180.00 ! GSP , from CG3C54 CG3C54 NG2R52 CG2R53, penalty= 55.9
OG3C51 CG3C53 NG2R52 CG2RC0     0.2500  3   180.00 ! GSP , from CG3C54 CG3C54 NG2R52 CG2R53, penalty= 59.9
HGA1   CG3C53 NG2R52 CG2R53     0.0000  3   180.00 ! GSP , from HGA2 CG3C54 NG2R52 CG2R53, penalty= 4
HGA1   CG3C53 NG2R52 CG2RC0     0.0000  3   180.00 ! GSP , from HGA2 CG3C54 NG2R52 CG2R52, penalty= 7
NG2R52 CG3C53 OG3C51 CG3C51     0.0000  3     0.00 ! GSP , from NG2R51 CG3C51 OG3C51 CG3C51, penalty= 34
PG1    OG304  PG0    OG311      0.1000  2     0.00 ! GSP , from PG0 OG304 PG0 OG311, penalty= 2
PG1    OG304  PG0    OG311      0.0300  3     0.00 ! GSP , from PG0 OG304 PG0 OG311, penalty= 2
PG1    OG304  PG0    SG2P1      0.0300  3     0.00 ! GSP , from PG0 OG304 PG0 SG2P1, penalty= 2
PG0    OG304  PG1    OG2P1      0.1000  2     0.00 ! GSP , from PG1 OG304 PG1 OG2P1, penalty= 2
PG0    OG304  PG1    OG2P1      0.0300  3     0.00 ! GSP , from PG1 OG304 PG1 OG2P1, penalty= 2
PG0    OG304  PG1    OG304      0.0300  2     0.00 ! GSP , from PG1 OG304 PG1 OG304, penalty= 2
PG0    OG304  PG1    OG304      0.0300  3     0.00 ! GSP , from PG1 OG304 PG1 OG304, penalty= 2

IMPROPERS

END

My topology file

* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 2.5.1
*
36 1

! "penalty" is the highest penalty score of the associated parameters.
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.

RESI GSP           -1.000 ! param penalty=  59.900 ; charge penalty=  57.254
GROUP            ! CHARGE   CH_PENALTY
ATOM P1     PG0     1.553 !    2.390
ATOM O1     OG304  -0.685 !    2.651
ATOM S      SG2P1  -0.620 !    0.632
ATOM O2     OG311  -0.648 !    0.632
ATOM O3     OG311  -0.648 !    0.632
ATOM P2     PG1     1.318 !    2.686
ATOM O4     OG2P1  -0.847 !    0.760
ATOM O5     OG2P1  -0.847 !    0.760
ATOM P3     PG1     1.505 !    0.000
ATOM O6     OG2P1  -0.816 !    0.000
ATOM O7     OG2P1  -0.816 !    0.000
ATOM O8     OG304  -0.764 !    0.912
ATOM O9     OG303  -0.621 !    0.000
ATOM C1     CG321  -0.081 !    0.000
ATOM C2     CG3C51  0.110 !   18.609
ATOM O10    OG3C51 -0.361 !   19.147
ATOM C3     CG3C51  0.141 !    2.325
ATOM O11    OG311  -0.651 !    0.000
ATOM C4     CG3C51  0.195 !   17.026
ATOM O12    OG311  -0.647 !   16.505
ATOM C5     CG3C53  0.072 !   56.641
ATOM N1     NG2R52 -0.048 !   57.254
ATOM C6     CG2R53  0.411 !    2.899
ATOM N2     NG2R52 -0.353 !   14.613
ATOM C7     CG2RC0  0.033 !   16.900
ATOM C8     CG2R63  0.573 !    2.500
ATOM O13    OG2D4  -0.454 !    0.000
ATOM N3     NG2R61 -0.249 !    0.000
ATOM C9     CG2R64  0.693 !    0.000
ATOM N4     NG2S3  -0.662 !    0.000
ATOM N5     NG2R62 -0.615 !    1.410
ATOM C10    CG2RC0  0.148 !   25.667
ATOM H1     HGP1    0.420 !    0.000
ATOM H2     HGP1    0.420 !    0.000
ATOM H3     HGA2    0.090 !    0.000
ATOM H4     HGA2    0.090 !    0.000
ATOM H5     HGA1    0.090 !    0.000
ATOM H6     HGA1    0.090 !    0.000
ATOM H7     HGP1    0.420 !    0.000
ATOM H8     HGA1    0.090 !    2.325
ATOM H9     HGP1    0.420 !    0.000
ATOM H10    HGA1    0.090 !    0.450
ATOM H11    HGR53   0.109 !    0.207
ATOM H12    HGP2    0.433 !    2.977
ATOM H13    HGP1    0.267 !    0.000
ATOM H14    HGP4    0.326 !    0.000
ATOM H15    HGP4    0.326 !    0.000

BOND P1   O1  
BOND P1   S   
BOND P1   O2  
BOND P1   O3  
BOND O1   P2  
BOND P2   O4  
BOND P2   O5  
BOND P2   O8  
BOND P3   O6  
BOND P3   O7  
BOND P3   O8  
BOND P3   O9  
BOND O9   C1  
BOND C1   C2  
BOND C2   O10 
BOND C2   C3  
BOND O10  C5  
BOND C3   O11 
BOND C3   C4  
BOND C4   O12 
BOND C4   C5  
BOND C5   N1  
BOND N1   C6  
BOND N1   C10 
BOND C6   N2  
BOND N2   C7  
BOND C7   C8  
BOND C7   C10 
BOND C8   O13 
BOND C8   N3  
BOND N3   C9  
BOND C9   N4  
BOND C9   N5  
BOND N5   C10 
BOND O2   H1  
BOND O3   H2  
BOND C1   H3  
BOND C1   H4  
BOND C2   H5  
BOND C3   H6  
BOND O11  H7  
BOND C4   H8  
BOND O12  H9  
BOND C5   H10 
BOND C6   H11 
BOND N2   H12 
BOND N3   H13 
BOND N4   H14 
BOND N4   H15 
IMPR C8     C7     N3     O13   
IMPR C9     N3     N5     N4    
IMPR N4     H15    H14    C9    

END
stefdoerr commented 10 months ago

Hi, you are missing the atom types in your parameter file (you can see it in the unknown atom type SG2P1 error). The topology file you are passing is not enough because it doesn't include the elements of the atoms. If you can upload the output folder in a zip I can give you more help.

H-EKE commented 10 months ago

Hi @stefdoerr

Thanks for your fast reply. If i am missing that atom type, why it appears in the "final" parameters file?

pre-build.zip p)

stefdoerr commented 10 months ago

It only appears in the dihedrals section but it's missing in the MASS section. Check as an example in the topologies folder the 7.toppar_water_ions_1.rtf. At the start it defines the masses of each atom type. You should do the same for the gsp_g.rtf file, define at the start the masses of your atom types.

Also make sure you are using the latest HTMD, I think you might be a version behind based on the parameters file which I'm seeing. Latest is 2.3.8 version.

H-EKE commented 10 months ago

Thank you so much!!