[gmx-users] tip4p2005 with gromacs 4.6.5

Justin Lemkul jalemkul at vt.edu
Wed Feb 17 23:48:50 CET 2016

On 2/17/16 5:41 PM, Irem Altan wrote:
> Hi,
> 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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