Errors regarding force field when using unknown residues

I'm trying to run the package on quite an unusual molecule and I thought that my .itp file was correct, however, I am starting to doubt this. When I run:

mdpow-equilibrium --solvent water runinput.yml

I was under the impression that mymolecule.itp was incorporated automatically by the package to the top of the topology file with #include. Or am I required to update the force field files myself aswell? If so, are these the ones in the MDPOW directory, or in the gromacs installation in /opt/gromacs/? (Apologies if this is more of a GROMACS question- I thought I'd ask here first because I'm not sure if I would be required to edit files within the gromacs installation or the MDPOW directory)

I get error messages implying that the force field has not been adapted to the new "residue":

ERROR 1 [file diaz.itp, line 26]:
  No default Bond types

ERROR 2 [file diaz.itp, line 27]:
  No default Bond types

ERROR 3 [file diaz.itp, line 30]:
  No default Bond types

ERROR 4 [file diaz.itp, line 53]:
  No default Angle types

ERROR 5 [file diaz.itp, line 54]:
  No default Angle types

ERROR 6 [file diaz.itp, line 57]:
  No default Angle types

ERROR 7 [file diaz.itp, line 58]:
  No default Angle types

ERROR 8 [file diaz.itp, line 59]:
  No default Angle types

ERROR 9 [file diaz.itp, line 60]:
  No default Angle types

ERROR 10 [file diaz.itp, line 62]:
  No default Angle types

ERROR 11 [file diaz.itp, line 64]:
  No default Angle types

ERROR 12 [file diaz.itp, line 66]:
  No default Angle types

ERROR 13 [file diaz.itp, line 67]:
  No default Angle types

ERROR 14 [file diaz.itp, line 68]:
  No default Angle types

ERROR 15 [file diaz.itp, line 69]:
  No default Angle types

ERROR 16 [file diaz.itp, line 70]:
  No default Angle types

ERROR 17 [file diaz.itp, line 71]:
  No default Angle types

ERROR 18 [file diaz.itp, line 76]:
  No default Ryckaert-Bell. types

ERROR 19 [file diaz.itp, line 79]:
  No default Ryckaert-Bell. types

ERROR 20 [file diaz.itp, line 80]:
  No default Ryckaert-Bell. types

ERROR 21 [file diaz.itp, line 82]:
  No default Ryckaert-Bell. types

ERROR 22 [file diaz.itp, line 83]:
  No default Ryckaert-Bell. types

grompp_qtot() failed. See warning and screen output for clues.

I assume grumpp_qtot is failing because of these errors, or should I change my qtot to an integer, I didn't think this was actually essential.

Here is my .ipt and .yml file my .ipt file:

[ moleculetype ]
; Name            nrexcl
DIA                 3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1   opls_135      1    DIA      C      1     -0.180   12.01100                             
     2   opls_906      1    DIA      C      2      0.060   12.01100                             
     3   opls_900      1    DIA      N      3     -0.900   14.00670                             
     4   opls_909      1    DIA      H      3      0.360    1.00800                             
     5   opls_909      1    DIA      H      3      0.360    1.00800                             
     6   opls_900      1    DIA      N      4     -0.900   14.00670                             
     7   opls_909      1    DIA      H      4      0.360    1.00800                             
     8   opls_909      1    DIA      H      4      0.360    1.00800                             
     9   opls_145      1    DIA      C      5     -0.115   12.01100                             
    10   opls_146      1    DIA      H      5      0.115    1.00800                             
    11   opls_154      1    DIA      O      5     -0.683   15.99940                             
    12   opls_155      1    DIA      H      5      0.418    1.00800                             
    13   opls_236      1    DIA      O      5     -0.500   15.99940                             

[ bonds ]
;  ai    aj funct
    1     2     1   ;     C     C
    1     3     1   ;     C     N
    1     4     1   ;     C     H
    1     5     1   ;     C     H
    2     6     1   ;     C     N
    2     9     1   ;     C     C
    2    10     1   ;     C     H
    3     6     1   ;     N     N
    3     8     1   ;     N     H
    6     7     1   ;     N     H
    9    11     1   ;     C     O
    9    13     1   ;     C     O
   11    12     1   ;     O     H

[ pairs ]
;  ai    aj funct
    2     6     1   ;     C     N
    2     8     1   ;     C     H
    1     7     1   ;     C     H
    1    11     1   ;     C     O
    1    13     1   ;     C     O
    1     7     1   ;     N     H
    6    11     1   ;     N     O
    6    13     1   ;     N     O
    2    12     1   ;     C     H

[ angles ]
;  ai    aj    ak funct
    2     1     3     1 ;     C     C     N
    2     1     4     1 ;     C     C     H
    2     1     5     1 ;     C     C     H
    1     2     6     1 ;     C     C     N
    1     2     9     1 ;     C     C     C
    1     2    10     1 ;     C     C     H
    3     1     4     1 ;     N     C     H
    3     1     5     1 ;     N     C     H
    1     3     6     1 ;     N     C     N
    1     3     8     1 ;     N     C     H
    4     1     5     1 ;     H     C     H
    6     2     9     1 ;     N     C     C
    6     2    10     1 ;     N     C     H
    2     6     7     1 ;     N     C     H
    9     2    10     1 ;     C     C     H
    2     9    11     1 ;     C     C     O
    2     9    13     1 ;     C     C     O
    6     3     8     1 ;     N     N     H
    3     6     7     1 ;     N     N     H
   11     9    13     1 ;     O     C     O
    9    11    12     1 ;     O     C     H

[ dihedrals ]
;  ai    aj    ak    al funct
    2     1     3     6     3   ;     C     C     N     N
    2     1     3     8     3   ;     C     C     N     H
    1     2     6     7     3   ;     C     C     N     H
    1     2     9    11     3   ;     C     C     C     O
    1     2     9    13     3   ;     C     C     C     O
    1     3     6     7     3   ;     N     C     N     H
    6     2     9    11     3   ;     N     C     C     O
    6     2     9    13     3   ;     N     C     C     O
    2     9    11    12     3   ;     C     C     O     H

[ dihedrals ]
;  aj    ak    ai    al funct
    1     6     3     8     1    improper_Z_N_X_Y   ;     H     C     N     N
    2     7     6     3     1    improper_Z_N_X_Y   ;     N     C     H     N
    2    13     9    11     1    improper_O_C_X_Y   ;     O     C     O     C

My .yml file:

DEFAULT:
  qscripts: local.sh
FEP:
  maxwarn: 0
  mdp: bar_opls.mdp
  method: BAR
  qscript: local.sh
  runlocal: true
  runtime: 5000
FEP_schedule_Coulomb:
  couple_lambda0: vdw-q
  couple_lambda1: vdw
  description: dis-charging vdw+q --> vdw
  label: Coul
  lambdas: 0, 0.25, 0.5, 0.75, 1.0
  name: Coulomb
  sc_alpha: 0
  sc_power: 1
  sc_sigma: 0.3
FEP_schedule_VDW:
  couple_lambda0: vdw
  couple_lambda1: none
  description: decoupling vdw --> none
  label: VDW
  lambdas: 0.0, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9,
    0.95, 1
  name: vdw
  sc_alpha: 0.5
  sc_power: 1
  sc_sigma: 0.3
MD_NPT:
  mdp: NPT_opls.mdp
  qscript: local.sh
  runlocal: true
  runtime: 50000
MD_relaxed:
  mdp: NPT_opls.mdp
  qscript: local.sh
  runlocal: true
  runtime: 5
energy_minimize:
  mdp: em_opls.mdp
mdrun:
  maxthreads: None
  nice: 19
  stepout: 1000
  verbose: true
setup:
  boxtype: dodecahedron
  distance: None
  forcefield: OPLS-AA
  gromacsoutput: false
  itp: "/Users/mark/Desktop/diaz/diaz.itp"
  maxwarn: 0
  molecule: dia
  name: diaz
  prm: None
  solventmodel: tip4p
  structure: "/Users/mark/Desktop/diaz/diaz.pdb"

Another quick question, what is the prm parameter in the setup section of the yml file (it is not present in the benzene tutorial example)?

Thank you very much for any assistance, it is greatly appreciated.

Can you provide here the corresponding .pdb file, please? What was the source of your .itp file?

Your .itp file is not complete, it has some missing values that are absent from the original OPLS-AA force field. I will give more explanations after providing the .pdb file, it will be easier.

Another quick question, what is the prm parameter in the setup section of the yml file (it is not present in the benzene tutorial example)?

The CHARMM/CGenFF force field requires a third (.prm) file, in addition to .itp and .pdb.

Can you provide here the corresponding .pdb file, please?

Since I cannot attach the file itself, I have uploaded it here: https://filebin.net/wf9jxtjbrd0zt1em If there is a file share site you would rather I use, let me know, this was what google recommended. I generated the pdb file with Avogadro, probably not the lowest energy structure, but I just wanted to use it as a test run.

What was the source of your .itp file?

I used topolgen-1.0 (found here: http://www.gromacs.org/Downloads/User_contributions/Other_software) to generate the itp file. I know the values produced are likely far off what they should be, but I thought it would just lead to inaccurate results, not total failure. There are so many sites that claim to generate itp files from pdb files, are there any you would recommend, or is it very situational?

EDIT: In the next comment I use another source, which looks like it contains more information...

The CHARMM/CGenFF force field requires a third (.prm) file, in addition to .itp and .pdb.

Ah alright, good to know.

Many thanks for the guidance.

I found an itp generator that looks more reliable (PRODRG - I don't think this is really suitable for all atoms force fields though, since it excludes hydrogens on carbon) and I see what you mean about the missing values before, however some of those look a bit too large.. and when I compare it to the itp files from your SAMPL6 data, it looks a bit excessive.. NEW itp file:

; Name nrexcl
DIA      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1        OM     1  DIA     OXT     1   -0.360  15.9994   
     2         C     1  DIA       C     1    0.720  12.0110   
     3        OM     1  DIA       O     1   -0.360  15.9994   
     4       CH1     1  DIA      CA     2    0.000  13.0190   
     5       CH1     1  DIA      CB     3    0.000  14.0270   
     6        NL     1  DIA     NAC     4   -0.280  14.0067   
     7         H     1  DIA     HAC     4    0.280   1.0080   
     8        NL     1  DIA       N     5   -0.280  14.0067   
     9         H     1  DIA       H     5    0.280   1.0080   

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.125  13400000.0    0.125  13400000.0 ;     C  OXT   
   2   3   2    0.125  13400000.0    0.125  13400000.0 ;     C    O   
   4   2   2    0.153   7150000.0    0.153   7150000.0 ;    CA    C   
   4   5   2    0.152   5430000.0    0.152   5430000.0 ;    CA   CB   
   4   8   2    0.147   8710000.0    0.147   8710000.0 ;    CA    N   
   5   6   2    0.147   8710000.0    0.147   8710000.0 ;    CB  NAC   
   6   7   2    0.100  18700000.0    0.100  18700000.0 ;   NAC  HAC   
   6   8   2    0.135   9412565.2    0.135   9412565.2 ;   NAC    N   
   8   9   2    0.100  18700000.0    0.100  18700000.0 ;     N    H   

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   5   1                                           ;   OXT   CB   
   1   8   1                                           ;   OXT    N   
   2   6   1                                           ;     C  NAC   
   2   9   1                                           ;     C    H   
   3   5   1                                           ;     O   CB   
   3   8   1                                           ;     O    N   
   4   7   1                                           ;    CA  HAC   
   5   9   1                                           ;    CB    H   
   7   9   1                                           ;   HAC    H   

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    126.0       770.0    126.0       770.0 ;   OXT    C    O   
   1   2   4   2    117.0       635.0    117.0       635.0 ;   OXT    C   CA   
   3   2   4   2    117.0       635.0    117.0       635.0 ;     O    C   CA   
   2   4   5   2    109.5       520.0    109.5       520.0 ;     C   CA   CB   
   2   4   8   2    109.5       285.0    109.5       285.0 ;     C   CA    N   
   5   4   8   2     90.0       418.4     90.0       418.4 ;    CB   CA    N   
   4   5   6   2     90.0       418.4     90.0       418.4 ;    CA   CB  NAC   
   5   6   7   2    109.5       425.0    109.5       425.0 ;    CB  NAC  HAC   
   5   6   8   2     90.0       418.4     90.0       418.4 ;    CB  NAC    N   
   7   6   8   2    109.5       380.0    109.5       380.0 ;   HAC  NAC    N   
   4   8   6   2     90.0       418.4     90.0       418.4 ;    CA    N  NAC   
   4   8   9   2    109.5       425.0    109.5       425.0 ;    CA    N    H   
   6   8   9   2    109.5       380.0    109.5       380.0 ;   NAC    N    H   

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   2   1   3   4   2      0.0  167.4        0.0  167.4   ; imp     C  OXT    O   CA   
   4   2   5   8   2     35.3  334.8       35.3  334.8   ; imp    CA    C   CB    N   
   6   5   8   7   2     35.3  334.8       35.3  334.8   ; imp   NAC   CB    N  HAC   
   8   4   6   9   2     35.3  334.8       35.3  334.8   ; imp     N   CA  NAC    H   
   8   4   2   1   1      0.0    1.0 6      0.0    1.0 6 ; dih     N   CA    C  OXT   
   6   5   4   2   1      0.0    5.9 3      0.0    5.9 3 ; dih   NAC   CB   CA    C   
   2   4   8   9   1      0.0    3.8 3      0.0    3.8 3 ; dih     C   CA    N    H   
   4   5   6   8   1      0.0    3.8 3      0.0    3.8 3 ; dih    CA   CB  NAC    N   
   5   6   8   9   1      0.0    3.8 3      0.0    3.8 3 ; dih    CB  NAC    N    H

Unfortunately, I still see errors, less of them, but it seems one of the atom types is still not recognised:

mdpow       : INFO     MDPOW 0.7.0-dev starting.
mdpow       : INFO     Copyright (c) 2010-2016 Ian Kenney, Bogdan Iorga, and Oliver Beckstein
mdpow       : INFO     Released under the GNU Public Licence, version 3.
mdpow       : INFO     For bug reports and help: https://github.com/Becksteinlab/MDPOW/issues
gromacs     : INFO     GromacsWrapper 0.8.0 STARTED logging to 'gromacs.log'
gromacs     : INFO     GromacsWrapper 0.8.0 STARTED logging to 'gromacs.log'
mdpow.config: INFO     Using the bundled force fields from GMXLIB='/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/top'.
mdpow.config: INFO     If required, override this behaviour by setting the environment variable GMXLIB yourself.
mdpow.run   : INFO     Selected solvent model: tip4p
gromacs.utilities: INFO     Working in '/Users/mark/Desktop/diaz/diaz/Equilibrium/water/top' (newly created)...
gromacs.utilities: INFO     Working in '/Users/mark/Desktop/diaz/diaz/Equilibrium/water/top' (newly created)...
gromacs.cbook: INFO     editing txt = '/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/templates/system.top' (9 substitutions)
gromacs.cbook: INFO     editing txt = '/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/templates/system.top' (9 substitutions)
gromacs.cbook: INFO     edited txt = 'system.top'
gromacs.cbook: INFO     edited txt = 'system.top'
mdpow.equil : INFO     [/Users/mark/Desktop/diaz/diaz/Equilibrium/water/top] Created topology 'system.top' that includes 'diaz.itp'
gromacs.utilities: INFO     Working in '/Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation' (newly created)...
gromacs.utilities: INFO     Working in '/Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation' (newly created)...
gromacs.setup: INFO     [/Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation] Solvating with water 'tip4p.gro'...
gromacs.setup: INFO     [/Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation] Solvating with water 'tip4p.gro'...
                      :-) GROMACS - gmx editconf, 2020 (-:

                            GROMACS is written by:
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 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf      Artem Zhmurov   
                           and the project leaders:
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Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
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as published by the Free Software Foundation; either version 2.1
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GROMACS:      gmx editconf, version 2020
Executable:   /usr/local/opt/gromacs/bin/gmx
Data prefix:  /usr/local/opt/gromacs
Working dir:  /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation
Command line:
  gmx editconf -f /Users/mark/Desktop/diaz/diaz.pdb -o boxed.gro -bt dodecahedron -d 1.0

Note that major changes are planned in future for editconf, to improve usability and utility.
WARNING: all CONECT records are ignored
Read 13 atoms
No velocities found
    system size :  0.415  0.434  0.278 (nm)
    diameter    :  0.498               (nm)
    center      : -0.028  0.390 -0.007 (nm)
    box vectors :  0.000  0.000  0.000 (nm)
    box angles  :   0.00   0.00   0.00 (degrees)
    box volume  :   0.00               (nm^3)
    shift       :  1.901  1.484  0.890 (nm)
new center      :  1.873  1.873  0.883 (nm)
new box vectors :  2.498  2.498  2.498 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :  11.02               (nm^3)

GROMACS reminds you: "Stupidity got us into this mess, and stupidity will get us out." (Homer Simpson)

                      :-) GROMACS - gmx solvate, 2020 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf      Artem Zhmurov   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx solvate, version 2020
Executable:   /usr/local/opt/gromacs/bin/gmx
Data prefix:  /usr/local/opt/gromacs
Working dir:  /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation
Command line:
  gmx solvate -cs tip4p.gro -p /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/system.top -cp boxed.gro -o solvated.gro

Reading solute configuration
Reading solvent configuration

Initialising inter-atomic distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------

Generating solvent configuration
Will generate new solvent configuration of 2x2x1 boxes
Solvent box contains 1840 atoms in 460 residues
Removed 160 solvent atoms due to solvent-solvent overlap
Removed 8 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
    SOL (   4 atoms):   418 residues
Generated solvent containing 1672 atoms in 418 residues
Writing generated configuration to solvated.gro

Output configuration contains 1685 atoms in 419 residues
Volume                 :      11.019 (nm^3)
Density                :     1150.51 (g/l)
Number of solvent molecules:    418   

Processing topology
Adding line for 418 solvent molecules with resname (SOL) to topology file (/Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/system.top)

Back Off! I just backed up /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/system.top to /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/#system.top.1#

GROMACS reminds you: "There is nothing new to be discovered in physics now. All that remains is more and more precise measurement." (Lord Kelvin, 1900)

gromacs.setup: INFO     Solvated system with tip4p.gro
gromacs.setup: INFO     Solvated system with tip4p.gro
/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py:568: GromacsFailureWarning: Gromacs tool failed
Command invocation: gmx grompp -p /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/system.top -c /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation/solvated.gro -o topol.tpr -f none.mdp
Error code: 1

  warnings.warn(msg + '\nError code: {0!r}\n'.format(rc), category=GromacsFailureWarning)
gromacs.cbook: ERROR    grompp_qtot() failed. See warning and screen output for clues.
gromacs.cbook: ERROR    grompp_qtot() failed. See warning and screen output for clues.
=========== grompp (stdout/stderr) ============

                       :-) GROMACS - gmx grompp, 2020 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
    Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra       Alan Gray     
  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
    Pascal Merz     Pieter Meulenhoff    Teemu Murtola       Szilard Pall   
    Sander Pronk      Roland Schulz      Michael Shirts    Alexey Shvetsov  
   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf      Artem Zhmurov   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, version 2020
Executable:   /usr/local/opt/gromacs/bin/gmx
Data prefix:  /usr/local/opt/gromacs
Working dir:  /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation
Command line:
  gmx grompp -p /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/system.top -c /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation/solvated.gro -o topol.tpr -f none.mdp

NOTE 1 [file none.mdp]:
  For a correct single-point energy evaluation with nsteps = 0, use
  continuation = yes to avoid constraining the input coordinates.

Setting the LD random seed to 615311803
Generated 342378 of the 342378 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 342378 of the 342378 1-4 parameter combinations

ERROR 1 [file diaz.itp, line 7]:
  Atomtype OM not found

There was 1 note

-------------------------------------------------------
Program:     gmx grompp, version 2020
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1408)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
===============================================
Traceback (most recent call last):
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-equilibrium", line 62, in <module>
    S = equilibrium_simulation(cfg, opts.solvent, dirname=opts.dirname)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/run.py", line 227, in equilibrium_simulation
    maxwarn=maxwarn)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/equil.py", line 394, in solvate
    params = self._setup_solvate(**kwargs)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/equil.py", line 348, in _setup_solvate
    return gromacs.setup.solvate(**kwargs)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/setup.py", line 626, in solvate
    **kwargs)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/setup.py", line 455, in solvate_ion
    p=topology, stdout=False, maxwarn=grompp_maxwarn)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/cbook.py", line 629, in grompp_qtot
    raise GromacsError(rc, msg)
gromacs.exceptions.GromacsError: [Errno 1] grompp_qtot() failed. See warning and screen output for clues.

I thought I'd post this, as a slightly closer attempt, with 1 atom type error, but still with the qtot error. Again, any guidance you can provide is greatly appreciated.

gromacs.log mdpow.log

I believe I may have solved this issue, using the LigParGen web server, I will close the thread when sure.

LigParGen should give you a correct input file. I paste below an example of a compound that we have used for the SAMPL7 Physical Properties challenge.

I will write you about your molecule later, in a separate post, as the answer requires more time.

;
; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University 
;
[ atomtypes ]
  opls_805  C805    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_817  C817    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_833  H833     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_823  H823     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_828  H828     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_814  C814    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_821  H821     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_827  H827     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_812  C812    12.0110     0.000    A    3.50000E-01   2.76144E-01
  opls_811  O811    15.9990     0.000    A    2.96000E-01   7.11280E-01
  opls_818  C818    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_829  H829     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_816  C816    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_826  H826     1.0080     0.000    A    2.50000E-01   1.25520E-01
  opls_809  C809    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_819  C819    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_804  C804    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_831  H831     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_800  O800    15.9990     0.000    A    2.96000E-01   8.78640E-01
  opls_806  C806    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_813  C813    12.0110     0.000    A    3.50000E-01   2.76144E-01
  opls_824  H824     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_815  C815    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_801  C801    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_834  H834     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_807  C807    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_810  O810    15.9990     0.000    A    2.96000E-01   7.11280E-01
  opls_825  H825     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_803  S803    32.0600     0.000    A    3.55000E-01   1.04600E+00
  opls_802  N802    14.0070     0.000    A    3.25000E-01   7.11280E-01
  opls_832  H832     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_820  H820     1.0080     0.000    A    0.00000E+00   0.00000E+00
  opls_822  H822     1.0080     0.000    A    2.42000E-01   1.25520E-01
  opls_808  C808    12.0110     0.000    A    3.55000E-01   2.92880E-01
  opls_830  H830     1.0080     0.000    A    2.42000E-01   1.25520E-01
[ moleculetype ]
; Name               nrexcl
UNK                   3
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  
     1   opls_800      1    UNK   O00      1    -0.3694    15.9990 
     2   opls_801      1    UNK   C01      1     0.8463    12.0110 
     3   opls_802      1    UNK   N02      1    -1.8128    14.0070 
     4   opls_803      1    UNK   S03      1     1.6322    32.0600 
     5   opls_804      1    UNK   C04      1    -0.4694    12.0110 
     6   opls_805      1    UNK   C05      1    -0.0306    12.0110 
     7   opls_806      1    UNK   C06      1    -0.1684    12.0110 
     8   opls_807      1    UNK   C07      1    -0.0812    12.0110 
     9   opls_808      1    UNK   C08      1    -0.1634    12.0110 
    10   opls_809      1    UNK   C09      1    -0.0095    12.0110 
    11   opls_810      1    UNK   O0A      1    -0.5172    15.9990 
    12   opls_811      1    UNK   O0B      1    -0.5172    15.9990 
    13   opls_812      1    UNK   C0C      1    -0.1941    12.0110 
    14   opls_813      1    UNK   C0D      1    -0.1280    12.0110 
    15   opls_814      1    UNK   C0E      1    -0.0940    12.0110 
    16   opls_815      1    UNK   C0F      1    -0.1408    12.0110 
    17   opls_816      1    UNK   C0G      1    -0.1438    12.0110 
    18   opls_817      1    UNK   C0H      1    -0.1424    12.0110 
    19   opls_818      1    UNK   C0I      1    -0.1441    12.0110 
    20   opls_819      1    UNK   C0J      1    -0.1382    12.0110 
    21   opls_820      1    UNK   H0K      1     0.7306     1.0080 
    22   opls_821      1    UNK   H0M      1     0.1592     1.0080 
    23   opls_822      1    UNK   H0N      1     0.1562     1.0080 
    24   opls_823      1    UNK   H0O      1     0.1538     1.0080 
    25   opls_824      1    UNK   H0P      1     0.1601     1.0080 
    26   opls_825      1    UNK   H0Q      1     0.1826     1.0080 
    27   opls_826      1    UNK   H0R      1     0.1438     1.0080 
    28   opls_827      1    UNK   H0S      1     0.1438     1.0080 
    29   opls_828      1    UNK   H0T      1     0.1003     1.0080 
    30   opls_829      1    UNK   H0U      1     0.1003     1.0080 
    31   opls_830      1    UNK   H0V      1     0.1488     1.0080 
    32   opls_831      1    UNK   H0W      1     0.1525     1.0080 
    33   opls_832      1    UNK   H0X      2     0.1516     1.0080 
    34   opls_833      1    UNK   H0Y      2     0.1518     1.0080 
    35   opls_834      1    UNK   H0Z      2     0.1505     1.0080 
[ bonds ]
    2     1     1      0.1229 476976.000
    3     2     1      0.1335 410032.000
    4     3     1      0.1670 363171.200
    5     4     1      0.1770 284512.000
    6     5     1      0.1400 392459.200
    7     6     1      0.1400 392459.200
    8     7     1      0.1400 392459.200
    9     8     1      0.1400 392459.200
   10     5     1      0.1400 392459.200
   11     4     1      0.1440 585760.000
   12     4     1      0.1440 585760.000
   13     2     1      0.1522 265265.600
   14    13     1      0.1529 224262.400
   15    14     1      0.1510 265265.600
   16    15     1      0.1400 392459.200
   17    16     1      0.1400 392459.200
   18    17     1      0.1400 392459.200
   19    18     1      0.1400 392459.200
   20    15     1      0.1400 392459.200
   21     3     1      0.1010 363171.200
   22     6     1      0.1080 307105.600
   23     7     1      0.1080 307105.600
   24     8     1      0.1080 307105.600
   25     9     1      0.1080 307105.600
   26    10     1      0.1080 307105.600
   27    13     1      0.1090 284512.000
   28    13     1      0.1090 284512.000
   29    14     1      0.1090 284512.000
   30    14     1      0.1090 284512.000
   31    16     1      0.1080 307105.600
   32    17     1      0.1080 307105.600
   33    18     1      0.1080 307105.600
   34    19     1      0.1080 307105.600
   35    20     1      0.1080 307105.600
   10     9     1      0.1400 392459.200
   20    19     1      0.1400 392459.200

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3 
    1     2     3     1    122.900    669.440
    2     3     4     1    112.000    585.760
    3     4     5     1    103.000    836.800
    4     5     6     1    119.400    711.280
    5     6     7     1    120.000    527.184
    6     7     8     1    120.000    527.184
    7     8     9     1    120.000    527.184
    4     5    10     1    119.400    711.280
    3     4    11     1    107.000   1004.160
    3     4    12     1    107.000   1004.160
    1     2    13     1    120.400    669.440
    2    13    14     1    111.100    527.184
   13    14    15     1    114.000    527.184
   14    15    16     1    120.000    585.760
   15    16    17     1    120.000    527.184
   16    17    18     1    120.000    527.184
   17    18    19     1    120.000    527.184
   14    15    20     1    120.000    585.760
    2     3    21     1    119.800    292.880
    5     6    22     1    120.000    292.880
    6     7    23     1    120.000    292.880
    7     8    24     1    120.000    292.880
    8     9    25     1    120.000    292.880
    5    10    26     1    120.000    292.880
    2    13    27     1    109.500    292.880
    2    13    28     1    109.500    292.880
   13    14    29     1    110.700    313.800
   13    14    30     1    110.700    313.800
   15    16    31     1    120.000    292.880
   16    17    32     1    120.000    292.880
   17    18    33     1    120.000    292.880
   18    19    34     1    120.000    292.880
   15    20    35     1    120.000    292.880
   19    18    33     1    120.000    292.880
   14    13    27     1    110.700    313.800
    5     4    12     1    107.200    619.232
   18    17    32     1    120.000    292.880
    7     6    22     1    120.000    292.880
    6     5    10     1    120.000    527.184
   20    19    34     1    120.000    292.880
    5    10     9     1    120.000    527.184
   11     4    12     1    119.000    870.272
   15    14    30     1    109.500    292.880
   16    15    20     1    120.000    527.184
    8     7    23     1    120.000    292.880
   19    20    35     1    120.000    292.880
   10     9    25     1    120.000    292.880
    4     3    21     1    111.000    836.800
    3     2    13     1    116.600    585.760
    5     4    11     1    107.200    619.232
   15    14    29     1    109.500    292.880
    9    10    26     1    120.000    292.880
   29    14    30     1    107.800    276.144
   27    13    28     1    107.800    276.144
   15    20    19     1    120.000    527.184
    8     9    10     1    120.000    527.184
   14    13    28     1    110.700    313.800
   17    16    31     1    120.000    292.880
    9     8    24     1    120.000    292.880
   18    19    20     1    120.000    527.184

[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES 
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    20    15    14    16    4        180.000     10.460     2  
    10     5     4     6    4        180.000     10.460     2  
    13     2     1     3    4        180.000     43.932     2  
    21     3     2     4    4        180.000     10.460     2  
    25     9     8    10    4        180.000     10.460     2  
    35    20    15    19    4        180.000     10.460     2  
    31    16    15    17    4        180.000     10.460     2  
    26    10     5     9    4        180.000     10.460     2  
    24     8     7     9    4        180.000     10.460     2  
    34    19    18    20    4        180.000     10.460     2  
    23     7     6     8    4        180.000     10.460     2  
    33    18    17    19    4        180.000     10.460     2  
    22     6     5     7    4        180.000     10.460     2  
    32    17    16    18    4        180.000     10.460     2  

[ dihedrals ]
; PROPER DIHEDRAL ANGLES
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    9   10    5    6        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   10    5    6    7        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   20   19   18   17        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   10    9    8    7        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   19   20   15   16        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   18   19   20   15        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   19   18   17   16        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   18   17   16   15        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    8    9   10    5        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   20   15   16   17        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    9    8    7    6        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    8    7    6    5        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   17   16   15   14        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   19   20   15   14        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    9   10    5    4        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
    7    6    5    4        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   16   15   14   13        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   20   15   14   13        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   10    5    4    3        3       0.006  -4.199   3.213   0.979  -0.000   0.000
    6    5    4    3        3       0.006  -4.199   3.213   0.979  -0.000   0.000
   15   14   13    2        3      -4.234   7.222   1.908  -4.895  -0.000   0.000
    5    4    3    2        3      -2.897  11.182  12.410  -20.694  -0.000   0.000
   13    2    3    4        3      -3.431  -3.008  10.598  -4.159  -0.000   0.000
   14   13    2    3        3       0.734  -9.985  -0.791  10.042  -0.000   0.000
   14   13    2    1        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   21    3    2   13        3      20.502   0.000  -20.502  -0.000  -0.000   0.000
   21    3    2    1        3      20.502   0.000  -20.502  -0.000  -0.000   0.000
   21    3    4    5        3      -15.611   0.703  20.506  -5.598  -0.000   0.000
   21    3    4   11        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   21    3    4   12        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   22    6    7    8        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   24    8    7    6        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   34   19   18   17        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   31   16   17   18        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   26   10    9    8        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   22    6    5   10        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   33   18   19   20        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   35   20   19   18        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   24    8    9   10        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   23    7    6    5        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   25    9    8    7        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   31   16   15   20        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   34   19   20   15        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   32   17   18   19        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   32   17   16   15        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   26   10    5    6        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   33   18   17   16        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   25    9   10    5        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   23    7    8    9        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   35   20   15   16        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   35   20   15   14        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   31   16   15   14        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   32   17   16   31        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   34   19   18   33        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   26   10    9   25        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   24    8    7   23        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   23    7    6   22        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   35   20   19   34        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   25    9    8   24        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   33   18   17   32        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   26   10    5    4        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   22    6    5    4        3      30.334   0.000  -30.334  -0.000  -0.000   0.000
   28   13    2    3        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   27   13    2    3        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   27   13    2    1        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   28   13    2    1        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   29   14   15   16        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   29   14   15   20        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   30   14   15   20        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   30   14   15   16        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   30   14   13    2        3      -0.209  -0.628   0.000   0.837  -0.000   0.000
   29   14   13    2        3      -0.209  -0.628   0.000   0.837  -0.000   0.000
   27   13   14   15        3       0.967   2.900   0.000  -3.866  -0.000   0.000
   28   13   14   15        3       0.967   2.900   0.000  -3.866  -0.000   0.000
   29   14   13   27        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   29   14   13   28        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   30   14   13   28        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   30   14   13   27        3       0.628   1.883   0.000  -2.510  -0.000   0.000
   11    4    5    6        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   12    4    5    6        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   12    4    5   10        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   11    4    5   10        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   11    4    3    2        3       0.000   0.000   0.000  -0.000  -0.000   0.000
   12    4    3    2        3       0.000   0.000   0.000  -0.000  -0.000   0.000
    4    3    2    1        3      25.476   0.000  -25.476  -0.000  -0.000   0.000

[ pairs ]
     1     4    1
     2     5    1
     3     6    1
     4     7    1
     5     8    1
     4     9    1
     3    10    1
     2    11    1
     2    12    1
     6     9    1
     1    14    1
     7    10    1
     6    11    1
     4    13    1
     3    14    1
     2    15    1
     6    12    1
    10    11    1
    10    12    1
     1    21    1
     5    21    1
     4    22    1
     5    23    1
     1    27    1
    13    16    1
     1    28    1
     8    22    1
     6    24    1
     5    25    1
     4    26    1
     3    27    1
    14    17    1
     3    28    1
     2    29    1
    11    21    1
    10    22    1
     9    23    1
     7    25    1
     6    26    1
     2    30    1
    15    18    1
    14    19    1
    13    20    1
    12    21    1
    13    21    1
    10    24    1
     8    26    1
    16    19    1
    17    20    1
    15    27    1
    15    28    1
    22    23    1
    16    29    1
    14    31    1
    16    30    1
    23    24    1
    15    32    1
    24    25    1
    20    29    1
    18    31    1
    16    33    1
    15    34    1
    14    35    1
    20    30    1
    25    26    1
    20    31    1
    19    32    1
    17    34    1
    16    35    1
    20    33    1
    18    35    1
    27    29    1
    28    29    1
    27    30    1
    28    30    1
    31    32    1
    32    33    1
    33    34    1
    34    35    1

REMARK LIGPARGEN GENERATED PDB FILE
ATOM      1  O00 UNK     1       1.000   1.000   0.000
ATOM      2  C01 UNK     1      -0.224   1.000   0.000
ATOM      3  N02 UNK     1      -0.967   1.000   1.188
ATOM      4  S03 UNK     1      -0.315   0.850   2.715
ATOM      5  C04 UNK     1       0.916   2.120   2.804
ATOM      6  C05 UNK     1       0.537   3.459   2.664
ATOM      7  C06 UNK     1       1.519   4.450   2.680
ATOM      8  C07 UNK     1       2.863   4.100   2.834
ATOM      9  C08 UNK     1       3.230   2.761   2.973
ATOM     10  C09 UNK     1       2.254   1.770   3.012
ATOM     11  O0A UNK     1      -1.383   1.226   3.620
ATOM     12  O0B UNK     1       0.314  -0.449   2.804
ATOM     13  C0C UNK     1      -0.994   0.916  -1.301
ATOM     14  C0D UNK     1      -2.326   1.657  -1.334
ATOM     15  C0E UNK     1      -2.972   1.558  -2.695
ATOM     16  C0F UNK     1      -3.805   0.474  -3.005
ATOM     17  C0G UNK     1      -4.404   0.379  -4.264
ATOM     18  C0H UNK     1      -4.174   1.364  -5.221
ATOM     19  C0I UNK     1      -3.347   2.446  -4.920
ATOM     20  C0J UNK     1      -2.706   2.516  -3.683
ATOM     21  H0K UNK     1      -1.978   1.054   1.212
ATOM     22  H0M UNK     1      -0.508   3.731   2.544
ATOM     23  H0N UNK     1       1.240   5.495   2.571
ATOM     24  H0O UNK     1       3.627   4.873   2.845
ATOM     25  H0P UNK     1       4.279   2.488   3.050
ATOM     26  H0Q UNK     1       2.535   0.737   3.201
ATOM     27  H0R UNK     1      -1.139  -0.148  -1.521
ATOM     28  H0S UNK     1      -0.337   1.320  -2.083
ATOM     29  H0T UNK     1      -2.187   2.711  -1.061
ATOM     30  H0U UNK     1      -3.020   1.244  -0.593
ATOM     31  H0V UNK     1      -3.995  -0.306  -2.270
ATOM     32  H0W UNK     1      -5.047  -0.466  -4.495
ATOM     33  H0X UNK     1      -4.639   1.290  -6.201
ATOM     34  H0Y UNK     1      -3.201   3.235  -5.652
ATOM     35  H0Z UNK     1      -1.998   3.320  -3.495
TER 
CONECT    1    2 
CONECT    2    3 
CONECT    3    4 
CONECT    4    5 
CONECT    5    6 
CONECT    6    7 
CONECT    7    8 
CONECT    8    9 
CONECT    5   10 
CONECT    4   11 
CONECT    4   12 
CONECT    2   13 
CONECT   13   14 
CONECT   14   15 
CONECT   15   16 
CONECT   16   17 
CONECT   17   18 
CONECT   18   19 
CONECT   15   20 
CONECT    3   21 
CONECT    6   22 
CONECT    7   23 
CONECT    8   24 
CONECT    9   25 
CONECT   10   26 
CONECT   13   27 
CONECT   13   28 
CONECT   14   29 
CONECT   14   30 
CONECT   16   31 
CONECT   17   32 
CONECT   18   33 
CONECT   19   34 
CONECT   20   35 
CONECT    9   10 
CONECT   19   20 
END

Thanks,

I get 1 warning, which I am going to temporarily allow to see what happens:

WARNING 1 [file system.top, line 30]: 13 non-matching atom names atom names from /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/system.top will be used atom names from /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation/solvated.gro will be ignored

You should not neglect this warning. It means that the order of atoms is not the same in the input .pdb and .itp files. Reordering the atoms in .pdb according to the order from .itp should fix this.

Attached are the .pdb and .itp for your structure, using the original OPLS-AA atom types. You will note that, compared with your original .pdb file, the atoms were reordered according to the order from the .itp file.

Remarks:

the hydrazine moiety is not parametrized in OPLS-AA, I had to adapt manually the charge of the two nitrogen atoms from -0.780 into -0.580 (they are adapted from secondary amine)
all other atoms are from the original OPLS-AA force field (you can find them in /your_installation_folder/share/gromacs/top/oplsaa.ff/ffnonbonded.itp)
for bonds, angles, dihedrals and impropers, if no values are present in the .itp file it is assumed that these values are already included in the force field (in /your_installation_folder/share/gromacs/top/oplsaa.ff/ffbonded.itp). If this is not the case, you'll get the errors that you already had and you need to provide them manually in the .itp file (either by using the values from similar bonds/angles/dihedrals or by fitting, which is a much more complex procedure).
to better understand the relationship between atoms and bonded parameters: in /your_installation_folder/share/gromacs/top/oplsaa.ff/ffnonbonded.itp the first column is the OPLS atom type, and the second column is the corresponding AMBER-like atom type. The last one is more general, and corresponds to several OPLS atom types (e.g. all OPLS atom types for aliphatic carbons opls_138 (CH4), opls_135 (CH3), opls_136 (CH2), opls_137 (CH) and opls_139 (tetrasubstituted C) correspond to the AMBER-like atom type CT). These AMBER-like atom types are used to define the bonded parameters (in /your_installation_folder/share/gromacs/top/oplsaa.ff/ffbonded.itp).

I'll let you to explore all these and come back if you have questions.

Please report if the files attached (remove the .txt extension, which was necessary to be able to attach the files here) work correctly with MDPOW.

diaz.pdb.1.itp.txt diaz.pdb.1.pdb.txt

Remarks:

Thank you for these explanations, they are very helpful.

I'll let you to explore all these and come back if you have questions. Please report if the files attached (remove the .txt extension, which was necessary to be able to attach the files here) work correctly with MDPOW.

I am currently running the simulations using the corrected .itp file from LigParGen, but after this I will be sure to run yours (which looks like it came from a personal script) and report back. It will be interesting to see how the two compare, especially vs other LogP predictions such as those from QSAR methods.

Thanks again.

(which looks like it came from a personal script)

Yes, it was generated by a script called MOL2FF that we have developed in house. But given that there are quite many parameters that are absent from the OPLS-AA force field, it requires very often manual (expert) intervention on the output .itp file and therefore is not adapted for public usage.

Please report if the files attached (remove the .txt extension, which was necessary to be able to attach the files here) work correctly with MDPOW.

So I changed all the residue names to DIA (from PRO) to stop it confusing it with the proline residue (admittedly I should have done this with the pdb file first before creation of the itp file). This allows the mdpow-equiilibrium to proceed to completion.

However, when I try to run export GW_START_LOGGING=True mdpow-fep --solvent water runinput.yml, with equilibrium data from LigParGen, I encounter the following error. Since I was able to run the mdpow-fep step with the benzene example, is it likely a mistake that I am making and not anything else? I have been unable to resolve this and I was wondering if you have any recommendations? Output:

Program:     gmx grompp, version 2020
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 905)

Fatal error:
Did not find any molecules of type 'dia' for coupling

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Traceback (most recent call last):
  File "/Users/mark/opt/anaconda3/envs/mdpow/bin/mdpow-fep", line 61, in <module>
    S = fep_simulation(cfg, opts.solvent, dirname=opts.dirname)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/run.py", line 342, in fep_simulation
    maxwarn=cfg.getint("FEP", "maxwarn"))
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/fep.py", line 594, in setup
    foreign_lambdas=lambdas, **kwargs)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/fep.py", line 649, in _setup
    return gromacs.setup.MD(**kwargs)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/setup.py", line 1121, in MD
    return _setup_MD(dirname, **kwargs)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/setup.py", line 940, in _setup_MD
    gromacs.grompp(f=mdp, p=topology, c=structure, n=index, o=tpr, **unprocessed)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py", line 398, in __call__
    return self.run(*args, **kwargs)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py", line 178, in run
    results, p = self._run_command(*_args, **_kwargs)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py", line 611, in _run_command
    self.check_failure(result, command_string=p.command_string)
  File "/Users/mark/opt/anaconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py", line 566, in check_failure
    raise GromacsError(rc, msg)
gromacs.exceptions.GromacsError: [Errno 1] Gromacs tool failed
Command invocation: gmx grompp -c /Users/mark/Desktop/diaz/diaz/Equilibrium/water/MD_NPT/md.gro -f md.mdp -pp processed.top -o md.tpr -n /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation/main.ndx -p /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/pp_system.top -maxwarn 0

I don't quite know what to infer from the errors in the log files:

2021-01-27 14:36:01,418 gromacs.cbook WARNING  Not substituted in 'md.mdp': ['pp', 'maxwarn']
2021-01-27 14:36:01,419 gromacs.setup WARNING  Unprocessed mdp option are interpreted as options for grompp:
{'pp': 'processed.top', 'maxwarn': 0}

gromacs.log mdpow.log

Thank you again for your guidance.

Try to run manually the command provided at the end of the error message:

gmx grompp -c /Users/mark/Desktop/diaz/diaz/Equilibrium/water/MD_NPT/md.gro -f md.mdp -pp processed.top -o md.tpr -n /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation/main.ndx -p /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/pp_system.top -maxwarn 0

Maybe you should increase the maxwarn value?

Try to run manually the command provided at the end of the error message:

This outputs the following error: Error in user input: Invalid command-line options In command-line option -f File 'md.mdp' does not exist or is not accessible. The file could not be opened. Reason: No such file or directory (call to fopen() returned error code 2)

When I use the full directory path (putting /Users/mark/Desktop/diaz/diaz/Equilibrium/water/MD_NPT/ infront of md.mdp), the command does works, which makes me think my hierarchy structure is wrong.. even though I was able to run mdpow-equilbirum.

My directory hierarchy looks correct, I think, especially considering the FEP folder which is created before the error is in the right place, but I will double check.

Many thanks.

So I thought there might have been a problem with the data gathered from the 50ns mdpow-equilibrium data, because when I deleted it(moved into backup directory) and did a very short mdpow-equilbirum simulation, the data outputted from this short run worked with the fep step... The only difference I see in the folder hierarchy between a short run and a 50ns run, is the presence of a md_prev.cpt file in the 50ns MD_NPT folder, but to my understanding, this is just a checkpoint restart file outputted for longer runs? I am 99.9% sure my directory hierarchy is correct, because using data from a short run works without changing path. Could this problem be because I am running the -fep command in a separate terminal session to generation of the 50ns data(-equilibrium), whereas when I perform a short run to test, I immediately performed the -fep command?

I find this all very bizarre, because, like I said, when I put /Users/mark/Desktop/diaz/diaz/Equilibrium/water/MD_NPT/ infront of md.mdp in the following command and run this separately, the 50ns data does not error, which makes me think my first point is invalid:

gmx grompp -c /Users/mark/Desktop/diaz/diaz/Equilibrium/water/MD_NPT/md.gro -f md.mdp -pp processed.top -o md.tpr -n /Users/mark/Desktop/diaz/diaz/Equilibrium/water/solvation/main.ndx -p /Users/mark/Desktop/diaz/diaz/Equilibrium/water/top/pp_system.top -maxwarn 0

Any ideas on what might be going wrong?

Note: This is referring to simulations using LipParGen topology, I will use your topology in a run soon.

> Fatal error:
> Did not find any molecules of type 'dia' for coupling

I looked back to your last messages, and I'm surprised by this error. DIA should be in big caps, not in small caps. Could you please check in the .pdb, .itp, .yml files that DIA is in big caps everywhere? We need to find from where it comes this small caps 'dia' in your error messages (there are several occurrences).

When I use the full directory path (putting /Users/mark/Desktop/diaz/diaz/Equilibrium/water/MD_NPT/ infront of md.mdp), the command does works, which makes me think my hierarchy structure is wrong.. even though I was able to run mdpow-equilbirum.

My directory hierarchy looks correct, I think, especially considering the FEP folder which is created before the error is in the right place, but I will double check.

The command does work, but it's not the right md.mdp file. These command should be executed in the FEP folder, in /Users/mark/Desktop/diaz/diaz/FEP/water/VDW/0000 (see mdpow.log). It should work without the full path for md.mdp, and maybe you'll get a warning that would explain the error that you have.

So I thought there might have been a problem with the data gathered from the 50ns mdpow-equilibrium data, because when I deleted it(moved into backup directory) and did a very short mdpow-equilbirum simulation, the data outputted from this short run worked with the fep step... The only difference I see in the folder hierarchy between a short run and a 50ns run, is the presence of a md_prev.cpt file in the 50ns MD_NPT folder, but to my understanding, this is just a checkpoint restart file outputted for longer runs? I am 99.9% sure my directory hierarchy is correct, because using data from a short run works without changing path. Could this problem be because I am running the -fep command in a separate terminal session to generation of the 50ns data(-equilibrium), whereas when I perform a short run to test, I immediately performed the -fep command?

The presence of md_prev.cpt is normal for longer simulations. Running the commands from two different terminals (but not simultaneously) should not be a problem.

I find this all very bizarre, because, like I said, when I put /Users/mark/Desktop/diaz/diaz/Equilibrium/water/MD_NPT/ infront of md.mdp in the following command and run this separately, the 50ns data does not error, which makes me think my first point is invalid:

As I said in my previous message, this is the wrong md.mdp file, you should use the one from the FEP folder.

Have you tried with maxwarn 1 or higher as I suggested previously ?

Any ideas on what might be going wrong?

Note: This is referring to simulations using LipParGen topology, I will use your topology in a run soon.

Let's see if my suggestions bring any new information helping to understand the origin of the problem. Using LipParGen topology should not be a problem.

Let's see if my suggestions bring any new information helping to understand the origin of the problem.

I realise now what has happened: So my .yml file originally had lowercase dia in the setup section (a rookie error from me, I apologise). mdpow-equilibrium is allowed to proceed when this is the case. However when it comes to -fep, it will error. The reason I did not pick up on this earlier, is because when I first got the error, I believe that I went through the yml file and changed dia to DIA. But since the equilibrium files were created with lowercase dia, it was now too late to change it to uppercase, so my fep step was still erroring.

The presence of md_prev.cpt is normal for longer simulations. Running the commands from two different terminals (but not simultaneously) should not be a problem.

I thought this was the case, but thanks for confirming.

Have you tried with maxwarn 1 or higher as I suggested previously ?

I had tried this, but I guess since it was a Fatal error it didn't make a difference.

Thanks again for the guidance, it's a shame it took me so long to realise my blunder.

No problem. We all make mistakes and we are here to learn.

Please rerun the whole protocol with short simulation times (e.g. 1 ns for equilibrium and 100 ps for each FEP window) to confirm that everything runs smoothly. The resulting numbers will not be reliable as the simulations will not be converged, but this is only for checking that the whole protocol works correctly now in your hands.

Please also open an issue for checking that the ligand code is exactly the same in all input files (.pdb, .itp and .yml). As you said, when a user realizes a possible mistake at the FEP stage, it is already too late.

Please rerun the whole protocol with short simulation times (e.g. 1 ns for equilibrium and 100 ps for each FEP window) to confirm that everything runs smoothly. The resulting numbers will not be reliable as the simulations will not be converged, but this is only for checking that the whole protocol works correctly now in your hands.

The whole protocol (up to the failing analysis stage of md-pow, as previously mentioned) runs smoothly.

Please also open an issue for checking that the ligand code is exactly the same in all input files (.pdb, .itp and .yml). As you said, when a user realizes a possible mistake at the FEP stage, it is already too late.

I will do this now.

Thanks again.

Becksteinlab / MDPOW

Errors regarding force field when using unknown residues #130