[gmx-users] (no subject)

[Justin Lemkul]

On 12/25/19 11:14 PM, Najamuddin Memon wrote:
> It is not about to select numbers in drop down menu. You should write atom
> no of protein and ligand. For example your chain a is protein having 2000
> atoms. The atom no starts from 1 till 2000 for protein. And for chain b is
> your ligand and your ligand has 40 atoms it is from 2001 till 2040. You can
> see these atom no in .top file.

More easily, one can identify which residues reside in loops and simply 
select by residue by using make_ndx.

-Justin

> On Wed, Dec 25, 2019, 8:54 PM nupur munjal <nupurmunjal at gmail.com> wrote:
>
>> Hi,
>> i am trying to make the index file without loops and termini and using the
>> option protein and ligand that is 1 and 13 but the index file is formed
>> with the same as it is formed from the whole system.
>>
>> --
>> Kind Regards
>> Nupur Munjal
>> PhD Scholar (Bioinformatics)
>> Department of Biotechnology & Bioinformatics
>> Jaypee University of Information Technology
>> Waknaghat, Solan,India
>>
>> The only thing that overcomes hard luck is hard work - Harry Golden
>>
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>> 12/25/19,
>> 9:22:30 PM
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================