[gmx-users] pdb (CTAB) into .GRO

Smith, Micholas D. smithmd at ornl.gov
Mon Nov 6 00:21:20 CET 2017

Justin is right, x2top is not "smart" but it can get you in the point you in a helpful direction.


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Sunday, November 05, 2017 12:13 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] pdb (CTAB) into .GRO

On 11/3/17 10:38 AM, Smith, Micholas D. wrote:
> One thing to try is to build the CTAB molecule with gmx x2top. You'll need to be careful about what it produces, but it can be helpful.

The only word of caution here is that you have to still tell x2top what
everything's charges and connectivities are, meaning you have to
pre-parametrize those interactions. x2top isn't smart enough to actually
do the hardest work for you, it just spits out a topology with a quality
equal to what you tell it :)



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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