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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