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

Justin Lemkul jalemkul at vt.edu
Sun Nov 27 03:13:51 CET 2016

On 11/26/16 2:41 PM, Jonathan Phillips wrote:
> Hi,
> 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.

FWIW, we have a complete CHARMM36 + latest CGenFF available at our website to 
save you some pain: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

> pdb2gmx runs without error, however when I run grompp, I get this:
>> Program grompp, VERSION 5.0.4
>> Source code file:
> /var/tmp/portage/sci-chemistry/gromacs-5.0.4/work/gromacs-5.0.4/src/gromacs/gmxpreprocess/toppush.c,
> 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.

"bond_atomtype" means "an atom type used in a bonded interaction."

> 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 ]
> section)
>> 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?

The presence of an atom type in the .atp file is not enough.  That file is only 
ever read by pdb2gmx.  grompp needs parameters for all those atom types in 
ffnonbonded.itp.  So if it finds a bonded interaction that involves an atom type 
it doesn't know about (e.g. you have a type in ffbonded.itp but not 
ffnonbonded.itp, which I bet is the case here) you get a fatal error.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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