[gmx-users] Index file

[Shima Arasteh]

 I know that I can use pdb and build my index file. But I want to know the problem. What's the problem?

Sincerely,
Shima


________________________________
From: Chandan Choudhury <iitdckc at gmail.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, December 31, 2012 11:08 AM
Subject: Re: [gmx-users] Index file







On Mon, Dec 31, 2012 at 1:07 PM, Chandan Choudhury <iitdckc at gmail.com> wrote:


>
>
>
>
>On Mon, Dec 31, 2012 at 11:59 AM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:
>
>Dear all,
>>I had a .pdb file containing protein, popc, and ions. So I used editconf to make a .gro file. But when I want to make an index file, 2 CL ions are not identified, so I can not choose it.
>>
>>
>use make_ndx f .pdb

use make_ndx -f .pdb


>Sincerely,
>>Shima
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>
>
>
>--
>Chandan kumar Choudhury
>NCL, Pune
>
>INDIA 
>



--
Chandan kumar Choudhury
NCL, Pune

INDIA