[gmx-users] Unknown bond_atomtype when trying to use charm27 with cgenff

Jonathan Phillips 994phij at gmail.com
Sat Nov 26 20:41:45 CET 2016


I'm trying to run a simulation of a protein:ligand complex using chamm27
and cgenff2b7.  After a little hacking (I'm using a PRES), I've used
charmm2gromacs-pvm.py to convert cgenff2b7 to cgenff2b7.ff/, and then
combined that with the charmm27 forcefield that comes with gromacs.

pdb2gmx runs without error, however when I run grompp, I get this:

>Program grompp, VERSION 5.0.4
>Source code file:
line: 742
>Fatal error:
>Unknown bond_atomtype CG1N1
>For more information and tips for troubleshooting, please check the GROMACS
>website at http://www.gromacs.org/Documentation/Errors

I can't work out what bond_atomtype is, or exactly where I've been stupid.

I've checked that:

atomtypes.atp contains the following line
>CG1N1   12.01100 ;      for cyano group
(if it's relevant, this was generated by appending the cgen atomtypes file
to the charmm atomtypes file).

ffcgenbonded.itp contains the following lines (under the [ bondtypes ]
>CG1N1   CG2R61  1       0.1435  288696.0
>CG1N1   CG331   1       0.147   334720.0
>CG1N1   NG1T1   1       0.118   881150.4

charmm27cgen.ff/forcefield.itp contains
>#include "ffcgenbonded.itp"
topol.top contains
>#include "./charmm27cgen.ff/forcefield.itp"
grompp is being called with -p topol.top

All bonds containing a CG1N1 atom in cgen.rtp are to one of the three
atomtypes in ffcgenbonded.itp quoted above.

Also, my ligand doesn't contain residues that have a CG1N1 atom in them
(neither does my protein, surprise, surprise).

So I don't know why it's looking at CG1N1, and I don't know why there are
issues with this atomtype, and I don't know what a bond_atomtype is, which
leaves me rather stuck.

Does anybody have any suggestions?

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