[gmx-users] hydrogen atom parameter definition for charmm 36
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
> edit topology database,can anyone give me the details of *.hdb file
> 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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