Thank you David, I really appreciated your help. I will read your paper and try to go on. Thank you very much!
2007/7/27, David Mobley <[EMAIL PROTECTED]>: > > Hi, > > > I am trying to run some simulations in attempts to calculate binding > free > > energy between ligands and a protein using the FEP method, but until now > I > > did not have any success. I have been looking for bibliography over this > > subject, but, as you may know, there aren't many works about FEP. What I > > found is one job where the solvation of amino acids analogs was > calculated, > > but there wasn't any mention about the usage of the method in > protein-ligand > > systems. What I would like to ask is: Is it possible to develop work > over > > free energy calculations using the FEP method in protein-ligand systems? > > You might start with my recent JMB paper for references. > http://dx.doi.org/10.1016/j.jmb.2007.06.002. There are also recent > reviews of free energy calculations by Rodinger and Pomes, and by > David Kofke, as well as one by Michael Shirts, myself, and John > Chodera that will be out in Annual Reports in Computational Chemistry > that will be out soon. > > For that matter, any literature search on "free energy perturbation" > should turn up lots of hits. I get 2,600 in a Google scholar search on > the subject ( > http://scholar.google.com/scholar?hl=en&lr=&q=%22free+energy+perturbation%22&btnG=Search > ). > Lots of hits for alchemical free energy calculations and thermodynamic > integration as well. I'm not sure why you think there aren't many > publications on FEP. > > David > > > > Thanks a lot, > > Diego Nolasco > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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