Hi, you could have a look into http://www.hecbiosim.ac.uk/fesetup to set up your system.
It is late evening here so I will answer in more detail tomorrow. Cheers, Hannes. On Mon, 3 Oct 2016 19:57:07 +0000 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.