[gmx-users] pdb2gmx generate .itp file for each molecule

Justin Lemkul jalemkul at vt.edu
Wed Feb 24 15:47:29 CET 2016

On 2/23/16 10:31 PM, Ray Chao wrote:
> ​Hi, gmx users,
> I used materials studio to generate a .pdb file containing 160 PTFE chains,
> and then modified the oplsaa  forcefiled as Justin did. The pdb2gmx
> generated right .gro and .top files. But the problem is that it generated
> one .itp file for each molecule. Since there are 160 identical molecules in
> the .pdb file, each .itp file is exactly the same except that it named the
> molecules as "Other", "Other2",...,"Other160". So is there any way to tell
> gromacs that there are actually 160 identical molecules in the .pdb file?

Extract the coordinates of one molecule from the box and run pdb2gmx on that one 
molecule.  Change the number in [molecules] to 160.



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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