[gmx-users] Pro-lig under one molecule type
subhashree.rout at kiitbiotech.ac.in
Fri Feb 19 08:06:37 CET 2016
Ok, Thank you Sir. I am trying to check.
On Thu, Feb 18, 2016 at 7:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 2/18/16 6:23 AM, Subhashree Rout wrote:
>> Thank you Sir for your suggestions. But sir I am simulating only protein
>> 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>
>>> you can follow this tutorial ,you might seen it but missed the part of
>>> 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,
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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