[gmx-users] Index file

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Dec 31 09:17:07 CET 2012

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


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

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>Chandan kumar Choudhury
>NCL, Pune

Chandan kumar Choudhury
NCL, Pune


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