[gmx-users] Pro-lig under one molecule type

Justin Lemkul jalemkul at vt.edu
Thu Feb 18 14:41:11 CET 2016

On 2/18/16 6:23 AM, Subhashree Rout wrote:
> Thank you Sir for your suggestions. But sir I am simulating only protein in
> water where pdb2gmx itself generates topol.top and porse.itp files. The
> topol.top file is already have command to include .itp file generated by
> gmx. In editconf defining boxtype with cubic and dimension 1.0.

Nikhil's reply was to a different question, not yours.

Follow Mark's advice.  Your coordinates are clearly bad, but you won't figure 
out what's wrong until you visualize the system.  mdrun prints the location of 
the maximum force, which is usually an indicator of where the problem lies.


> On Thu, Feb 18, 2016 at 4:11 PM, Nikhil Maroli <scinikhil at gmail.com> wrote:
>> HI,
>> you can follow this tutorial ,you might seen it but missed the part of
>> topol.top
>> you have to include *itp files and Molecules in topology,it is very easy
>> There are lots of threads in this mailing list regarding this,
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-
>> tutorials/complex/
>> --
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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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