[gmx-users] tip4p2005 with gromacs 4.6.5
jalemkul at vt.edu
Wed Feb 17 23:48:50 CET 2016
On 2/17/16 5:41 PM, Irem Altan wrote:
> I would like to use TIP4P2005 with Gromacs 4.6.5 for a protein simulation with water. I have the .itp and .gro files for the model.
> I am using a slightly modified version of the Amber forcefields, so I have a folder called amber99sb.ff in my working directory. I have added a file called tip4p2005.itp into that folder. I then tried the following:
> pdb2gmx -f amber99sb.ff/ -water tip4p2005.itp -o box.gro -p topol.top
> as well as
> pdb2gmx -f amber99sb.ff/ -water tip4p2005 -o box.gro -p topol.top
> both of which result in an error saying “invalid argument tip4p2005(.itp) for option -water”.
> How can I get this to work?
It must match the first field of an entry in watermodels.dat in the force field
Also note that pdb2gmx -f takes a coordinate file, not a directory name. That
will cause a whole host of failures...
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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