[gmx-users] Index file

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Dec 31 17:20:40 CET 2012

No, I see CL ions in gro file after using editconf, but when I want to make an index file, there is not CL option to choose!


From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, December 31, 2012 6:02 PM
Subject: Re: [gmx-users] Index file

On 12/31/12 3:17 AM, Shima Arasteh wrote:
>   I know that I can use pdb and build my index file. But I want to know the problem. What's the problem?

It sounds rather unbelievable that editconf would mysteriously delete atoms. There is no way for anyone to say what is going on given the current information.  Please post:

1. Your editconf command
2. The first and last few lines of atoms section of the original .pdb file
3. The first and last few lines of the resulting .gro file


-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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