[gmx-users] binding energy calculation when appear this error: no distance restraints in topology

[fatemeh ramezani]

the command that I used is :

 g_energy    -f  md300.edr   -s  fws_md300.tpr    -o energy.xvg    -pairs     pairs.xvg  


Fatemeh Ramezani


________________________________
 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

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

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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