[gmx-users] binding energy calculation when appear this error: no distance restraints in topology
fr_750 at yahoo.com
Sun Apr 14 21:09:19 CEST 2013
the command that I used is :
g_energy -f md300.edr -s fws_md300.tpr -o energy.xvg -pairs pairs.xvg
From: Justin Lemkul <jalemkul at vt.edu>
To: fatemeh ramezani <fr_750 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, 14 April 2013, 21:15
Subject: Re: [gmx-users] binding energy calculation when appear this error: no distance restraints in topology
On 4/14/13 9:38 AM, fatemeh ramezani wrote:
> Dear all
> After simulation of gold-protein interaction, now I want to calculate binding energy of each residue to gold. but when I use g_energy command appear this error:
> No distance restraints in topology
> How can I calculate binding energy without running simulation again(because it takes about one week and I need this result as soon as possible) ?
Please provide the exact command you used. There is no reason for g_energy to be reading a topology to extract this information. You can get so-called "nonbonded interaction energies" decomposed by energy group, but whether or not you can call this an actual "binding energy" is highly questionable.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users