Cannot find the force fields that I put in a directory, working_dir/charmm36.ff

User discussions
1

GROMACS version:2023.3-PLUMED_spack
GROMACS modification: No
Here post your question

I’m running on a Cray super computer, so I don’t have write permissions in the $GMXLIB/share/gromacs/top
directory.

So I put the contents of the charmm force field download:
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
into a directory called
charmm36-jul2022.ff
inside my working directory (where I launch gmx_mpi)
But gmx_mpi pdb2gmx
does not find these force fields.

It only offers me force fields that it finds in Data Prefix /share/gromacs/top

Here is the output, which confirms my current working directory is where I launched the gmx_mpi command:

gmx_mpi pdb2gmx -ignh -f 6rhy_model1chainA.pdb -o 6rhy_processed.gro -water tip4p
:-) GROMACS - gmx pdb2gmx, 2023.3-PLUMED_spack (-:

Executable: /opt/software/gaia/prod/3.0.0/spack_path_placeholder/spack_path_placeholder/spack_path_placeholder/__spack_path_plac/gromacs-2023.3-cce-17.0.0-xogq/bin/gmx_mpi
Data prefix: /opt/software/gaia/prod/3.0.0/spack_path_placeholder/spack_path_placeholder/spack_path_placeholder/__spack_path_plac/gromacs-2023.3-cce-17.0.0-xogq

Working dir: /lus/home/CT7/cad15071/rscott/gromacs_charmm
Command line:
gmx_mpi pdb2gmx -ignh -f 6rhy_model1chainA.pdb -o 6rhy_processed.gro -water tip4p

Select the Force Field:

From ‘/opt/software/gaia/prod/3.0.0/spack_path_placeholder/spack_path_placeholder/spack_path_placeholder/__spack_path_plac/gromacs-2023.3-cce-17.0.0-xogq/share/gromacs/top’:

1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)

2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)

3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)

4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)

5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)

6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)

7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)

8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)

9: GROMOS96 43a1 force field

10: GROMOS96 43a2 force field (improved alkane dihedrals)

11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)

12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)

13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)

14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)

15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

And that’s all. No other options!

2

If you do “ls charmm36-jul2022.ff” what is the output? I.e. what are the contents of that directory?

3

ls -l charmm36-jul2022.ff/
total 13236
-rw-r–r–. 1 rscott cad15071 95 Dec 9 2022 aminoacids.arn
-rw-r–r–. 1 rscott cad15071 2079 Dec 9 2022 aminoacids.c.tdb
-rw-r–r–. 1 rscott cad15071 174309 Dec 9 2022 aminoacids.hdb
-rw-r–r–. 1 rscott cad15071 1794 Dec 9 2022 aminoacids.n.tdb
-rw-r–r–. 1 rscott cad15071 1757 Dec 9 2022 aminoacids.r2b
-rw-r–r–. 1 rscott cad15071 659106 Dec 9 2022 aminoacids.rtp
-rw-r–r–. 1 rscott cad15071 34057 Dec 9 2022 atomtypes.atp
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 carb.c.tdb
-rw-r–r–. 1 rscott cad15071 307419 Dec 9 2022 carb.hdb
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 carb.n.tdb
-rw-r–r–. 1 rscott cad15071 452 Dec 9 2022 carb.r2b
-rw-r–r–. 1 rscott cad15071 720411 Dec 9 2022 carb.rtp
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 cgenff.c.tdb
-rw-r–r–. 1 rscott cad15071 479269 Dec 9 2022 cgenff.hdb
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 cgenff.n.tdb
-rw-r–r–. 1 rscott cad15071 452 Dec 9 2022 cgenff.r2b
-rw-r–r–. 1 rscott cad15071 1243998 Dec 9 2022 cgenff.rtp
-rw-r–r–. 1 rscott cad15071 169911 Dec 9 2022 cmap.itp
-rw-r–r–. 1 rscott cad15071 1051 Dec 9 2022 ethers.c.tdb
-rw-r–r–. 1 rscott cad15071 10535 Dec 9 2022 ethers.hdb
-rw-r–r–. 1 rscott cad15071 1051 Dec 9 2022 ethers.n.tdb
-rw-r–r–. 1 rscott cad15071 452 Dec 9 2022 ethers.r2b
-rw-r–r–. 1 rscott cad15071 23804 Dec 9 2022 ethers.rtp
-rw-r–r–. 1 rscott cad15071 2475682 Dec 9 2022 ffbonded.itp
-rw-r–r–. 1 rscott cad15071 5467 Dec 9 2022 ffmissingdihedrals.itp
-rw-r–r–. 1 rscott cad15071 2691360 Dec 9 2022 ffnonbonded.itp
-rw-r–r–. 1 rscott cad15071 18804 Dec 9 2022 forcefield.doc
-rw-r–r–. 1 rscott cad15071 1004 Dec 9 2022 forcefield.itp
-rw-r–r–. 1 rscott cad15071 19183 Dec 9 2022 ions.itp
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 lipid.c.tdb
-rw-r–r–. 1 rscott cad15071 1511523 Dec 9 2022 lipid.hdb
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 lipid.n.tdb
-rw-r–r–. 1 rscott cad15071 452 Dec 9 2022 lipid.r2b
-rw-r–r–. 1 rscott cad15071 2581901 Dec 9 2022 lipid.rtp
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 metals.c.tdb
-rw-r–r–. 1 rscott cad15071 422 Dec 9 2022 metals.hdb
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 metals.n.tdb
-rw-r–r–. 1 rscott cad15071 452 Dec 9 2022 metals.r2b
-rw-r–r–. 1 rscott cad15071 1552 Dec 9 2022 metals.rtp
-rw-r–r–. 1 rscott cad15071 732 Dec 9 2022 na.c.tdb
-rw-r–r–. 1 rscott cad15071 44207 Dec 9 2022 na.hdb
-rw-r–r–. 1 rscott cad15071 1740 Dec 9 2022 na.n.tdb
-rw-r–r–. 1 rscott cad15071 677 Dec 9 2022 na.r2b
-rw-r–r–. 1 rscott cad15071 139255 Dec 9 2022 na.rtp
-rw-r–r–. 1 rscott cad15071 16484 Dec 9 2022 nbfix.itp
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 silicates.c.tdb
-rw-r–r–. 1 rscott cad15071 1037 Dec 9 2022 silicates.hdb
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 silicates.n.tdb
-rw-r–r–. 1 rscott cad15071 452 Dec 9 2022 silicates.r2b
-rw-r–r–. 1 rscott cad15071 4836 Dec 9 2022 silicates.rtp
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 solvent.c.tdb
-rw-r–r–. 1 rscott cad15071 576 Dec 9 2022 solvent.hdb
-rw-r–r–. 1 rscott cad15071 455 Dec 9 2022 solvent.n.tdb
-rw-r–r–. 1 rscott cad15071 452 Dec 9 2022 solvent.r2b
-rw-r–r–. 1 rscott cad15071 7155 Dec 9 2022 solvent.rtp
-rw-r–r–. 1 rscott cad15071 493 Dec 9 2022 spc.itp
-rw-r–r–. 1 rscott cad15071 502 Dec 9 2022 spce.itp
-rw-r–r–. 1 rscott cad15071 553 Dec 9 2022 tip3p.itp
-rw-r–r–. 1 rscott cad15071 545 Dec 9 2022 tip3p_original.itp
-rw-r–r–. 1 rscott cad15071 1011 Dec 9 2022 tip4p.itp
-rw-r–r–. 1 rscott cad15071 1366 Dec 9 2022 tip4pew.itp
-rw-r–r–. 1 rscott cad15071 2100 Dec 9 2022 tip5p.itp
-rw-r–r–. 1 rscott cad15071 348 Dec 9 2022 watermodels.dat

4

That looks fine, so I don’t know what’s wrong. You could try
gmx_mpi pdb2gmx -ignh -f 6rhy_model1chainA.pdb -o 6rhy_processed.gro -water tip4p -ff charmm36-jul2022
But I guess it will not work either.

If I were you, I’d contact the support staff of the super computer to see if they have any idea.

5

Hello Magnus

Actually your proposed solution, with the -ff charm36.ff in the command
line, did work for me. Thank you very much for your help.

In fact, I’m having trouble reproducing the original problem. The only
thing I changed was to provide the force field directory via a symbolic
link and now gmx_mpi finds them. I suspect there to be some instability
in the system; there was some “MANPATH” problem that I didn’t follow.

I’m sorry I troubled people for a transitory problem.

In any case, I’m very happy it’s working as described in the manual and
very grateful for your responses.

Best wishes,
Rob

ZpaumI0Ki04YR80w.png