[gmx-users] grompp

Justin Lemkul jalemkul at vt.edu
Thu Oct 15 13:27:51 CEST 2015

On 10/15/15 6:17 AM, badamkhatan togoldor wrote:
>   Dear Gmx Users,
> I have a question on grompp !
> I built some membrane in Charmm-gui with ion and water etc and i took that output data for gromacs. Then i changed xxxx.pdb file on the gromacs. Do the pdb2gmx and editconf then grompp. Unfortunately grompp gave me an error!
> No default U-B types.[file topol.top, line XXXX]
> In this case what should i do?( I thought charmm-gui generated and supplied all ffbonded.itp ( .itp files was in "toppor" directory ) file for this membrane. and then i should put it that file on gromacs' ffbonded. itp file ? ) What's the wrong in here? Any help or suggestion highly appreciate!       I am using charmm36.ff .

CHARMM-GUI provides you with all necessary GROMACS input files (coordinates, 
topology, .mdp) so there is no need to invoke pdb2gmx, editconf, etc.  Use the 
files it gives you and do not modify them.



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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