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

[Subhashree Rout]

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
>> 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.
>
> -Justin
>
> 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
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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-- 
Subhashree Rout
PhD Scholar
Bioinformatics Lab
KIIT School of Biotechnology
KIIT University
Bhubaneswar
Odisha
INDIA
Pin-751024