[gmx-users] Topology error

Justin Lemkul jalemkul at vt.edu
Tue Apr 7 18:49:35 CEST 2015

On 4/7/15 8:23 AM, Abid Channa wrote:
> Dear gromacs users, I am working on protein-ligand simulation, I have
> prepared ligand topology through PRODRG server, it is generating many files ,
> I am taking co-ordinate file Gromos-87/Gromacs (polar/aromatic hydrogens) and
> gromacs topoplogy file interms "drg.itp", problem is that PRODRG only take
> unprotonated form while I am giving input file with protonated form , prodrg
> delete all the hydrogens, my ligand has 58 atoms , while PRODRG only generate
> 36 atoms topoly and coordinate file, PRODRG also generate all hydrogen file
> when I take that file topolgy error occurs in topol.top file and solv.gro
> file,, waiting for comments from all of you specially from Justin ,,,,,

If there's a problem with protonation (note: this only applies to titratable 
groups), see the PRODRG FAQ.  It doesn't deal with ionization state well; you 
have to tell it what you want.

The rest is likely due to the fact that GROMOS is a united-atom force field; 
aliphatic hydrogens are not explicitly represented.

Take great care to refine any PRODRG-generated topology.  They're never usually 
very accurate.



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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