[gmx-users] Index file

[Shima Arasteh]

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!




Sincerely,
Shima


________________________________
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

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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