[gmx-users] water models

Irem Altan irem.altan at duke.edu
Thu Mar 3 23:49:49 CET 2016

The problem is, when I try to do pdb2gmx I get the following error:

Residue 'HO5' not found in residue topology database

On Mar 3, 2016, at 5:31 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

On 3/3/16 5:27 PM, Irem Altan wrote:

On Mar 3, 2016, at 5:06 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

On 3/3/16 2:21 PM, Irem Altan wrote:

I have two general questions about TIP5P and GROMACS version 5.1.2. (I am
using AMBER99SB).

- Is it normal that TIP5P does not work out of the box? When I do pdb2gmx
without modifying force field files, I get an error saying Residue 'HO5' not
found in residue topology database . This is really confusing, as there
exists a tip5p.gro, tip5p.itp, the LJ parameters exists within
ffnonbonded.itp, the atoms are defined in atomtypes.atp, but there is nothing
within aminoacids.rtp and aminoacids.hdb. Is it meant to be that way?

Normally the water topology is simply taken care of by #including the appropriate stock topology.  pdb2gmx will try to create bonds between the atoms, which is not normal for rigid water models.

So am I incorrect in creating relevant entries in aminoacids.rtp and aminoacids.hdb?

It certainly won't give you a rigid water model.  Process the protein with pdb2gmx, solvate with the available tip5p.gro and use tip5p.itp to describe the waters.



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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441

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