[gmx-users] hydrogen atom parameter definition for charmm 36

Justin Lemkul jalemkul at vt.edu
Sat Apr 9 14:50:14 CEST 2016

On 4/9/16 8:42 AM, Nikhil Maroli wrote:
> Dear all,
> i m doing mmpbsa calculation using GMXPBSA tool ,for protein ligand complex
> during the steps i invoked the command
>    pdb2gmx -f _comp0.pdb -p topol_comp.top -i posre_comp.itp -o _comp0.gro
> -ignh -water tip3p
> i have generated the ligand topology such as *.itp and *.prm file ,but it
> looks like i cant  insert those in topology as doing usually ,in order to

Why not?

> edit topology database,can anyone give me the details of *.hdb file
> example
> VAL     5
> 1   1   HN  N   -C  CA
> 1   5   HA  CA  N   C   CB
> 1   5   HB  CB  CA  CG1 CG2
> 3   4   HG1 CG1 CB  CA
> 3   4   HG2 CG2 CB  CA

The .hdb is only for constructing hydrogen positions; it has nothing to do with 
writing your topology.  If you already have a ligand topology, process the 
protein as normal and you don't have to fiddle with any of these files.

> what is HN N -C CA?

See the manual, section 5.7.4.



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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