[gmx-users] 4 question

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Aug 17 19:38:54 CEST 2012

Thanks Justin.


----- Original Message -----
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: Friday, August 17, 2012 10:07 PM
Subject: Re: [gmx-users] 4 question

On 8/17/12 1:33 PM, Shima Arasteh wrote:
> Hi,
> The .pdb file either should be dowloaded from RCSB website or you need to construct the structure by a software such as hyperchem and save the structure in .pdb format, so you are not supposed to get .pdb output through pdb2gmx command.

The output configuration produced by pdb2gmx can be any number of formats that the user chooses.  The .gro file format is default, but one can obtain .pdb, .g96, etc.  Gromacs programs accept and use numerous file formats.


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

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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