Mark, I've told about estimation of the energy of the ligands compounds (small hormone-like compounds) embedded in the receptors binding pocket.
In other words I want to simulate that ligands in water as well as in the receptor complex and compare it's potential energy values in both cases. From such experiment I want to check hypothesis that in the receptor interior the ligands always in more strained conformations ( with highter value of potential energy) than in the unbound state. James 2012/12/4, Mark Abraham <[email protected]>: > What components will that potential energy have? > > Mark > > On Mon, Dec 3, 2012 at 6:54 PM, James Starlight > <[email protected]>wrote: > >> Dear Gromacs Users! >> >> I'm simulating different complexes of the receptors with different >> ligands. >> >> For each complex I want to determine potential energy (not the binding >> energy) of the ligand molecule. In other words I want to check in what >> exactly complex ligand was in more or less strained conformation due >> to the binding pocket influence. How I could do such estimations ? >> >> Thanks for help >> >> >> James >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
