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 <jalem...@vt.edu> To: fatemeh ramezani <fr_...@yahoo.com>; Discussion list for GROMACS users <gmx-users@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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
