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Mark On Mon, Oct 3, 2016 at 9:57 PM Guanglin Kuang <guang...@kth.se> wrote: > Dear Gromacs users, > > Has any of you managed to use Gromacs to do relative free energy > calculations? I have some technical questions that would need your > suggestions. > > I am trying to reproduce the Amber free energy calculation using PMEMD ( > http://ambermd.org/tutorials/advanced/tutorial9/#overview). > > First, I generated the topology and coordinate files of the ligands > (benzene and phenol) using alchemistry_setup.py, developed by Dr. David > Mobley (https://github.com/MobleyLab/alchemical-setup), as well as > antechamber with AM1/BCC charge. > > Then I set up the mdp file and topology file for relative free energy > calculations. I used the single topology together with the one-step and > three-step transformations, respectively. Please have a look at the > relevant files attached for the details. > > Finally, I used g_bar to calculate the free energy > (alchemistry_analysis.py can give similar results). From the results I > found that one-step transformation can give good results, only if some > restraints are applied to the protein-ligand complex, because I found that > benzene/phenol are not strong binders to lyszome, and would drift around in > the binding pocket, thus give poor results deviating from experimental > data. However, in the three-step strategy, the results are much worse, this > is probably due to the fact that a dual topology is used in Amber but a > single topology is used in Gromacs (my case), we may not be able to do the > changes directly (as shown in the attached topology files). > > Even though one-step transformation seems to give a better result in this > case, it may be due to luck, because it is suggested that one-step > transformation is usually not as good as three-step transformation, and can > even give misleading results in some occasions (what occasions?). > > Therefore, could any experienced users of relative free energy calculation > have a look at my set-up and point out the problems? I would appreciate any > improvement to the set-up! > > Thank you! > > > ----------------------------------------------------------------------------------------------------------------------------------------------------------- > Best Regards! > Guanglin Kuang > KTH-Royal Institute of Technology > School of Biotechnology > Division of Theoretical Chemistry & Biology > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.