[gmx-users] CGennFF in gromacs

Justin Lemkul jalemkul at vt.edu
Thu Aug 29 02:34:11 CEST 2013

On 8/28/13 8:23 PM, Golshan Hejazi wrote:
> Hello everyone,
> I want to use CGennFF force field in GROMACS. I downloaded the Cgenffbon.itp and  Cgenffnb.itp files and I put them in charmm36.ff directory.
> - I replaced the lines in the forcefield.itp to #include "Cgenffbon.itp"  and #include "Cgenffnb.itp"
> - I modified the rtp file and I inserted the corresponding atom, bond, dihedral terms as in charmm rtf file for paracetamol in the rtp file in gromacs
> - I inserted the new atomtypes at the end of the atomtype.atp file ... I took the atom types from prm file of charmm
> - I introduced the new residue name to the residuetype file
> - with pdb2gmx ... I could generate the topol.top file without any error
> However, when I am using grompp, it give me the following error:
> Fatal error:
> Atomtype CG331 not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I already have this atomtype inside the atomtype file ... and when I was pdb2gmx ... it did not complain ! Can you help me to figure out what is going on?

That is the only time atomtypes.atp is used.  The error from grompp comes 
because it can't find CG331 in CGenffnb.itp, so check that file carefully.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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