[gmx-users] water models
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
- 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
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users