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

[Justin Lemkul]

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

-- 
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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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