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Best regards! Guanglin -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Monday, October 03, 2016 10:00 PM To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Gromacs Relative Free Energy Calculation Issue Hi, The list cannot accept attachments, so if you would like to share files, please do so via a file-sharing service, and post the links you wish to share :-) 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. -- 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.