Dear Hannes, Only the topology and coordinate of the mutated ligand is produced by FESetup. The topology file (lig_FE.top) is adapted from pert.atp and pert.itp, while the coordinate file is from morph.gro. Based on these two files, I set up the systems and did the simulations. The original files have been uploaded: https://drive.google.com/open?id=0B8f0-zVoaBXNWWtvYTIwU2ZBRGs Maybe I didn't use FESetup properly, could you have a look at the uploaded files please?
Thank you! 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 Hannes Loeffler Sent: Wednesday, October 05, 2016 12:28 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: gmx-us...@gromacs.org Subject: Re: [gmx-users] Gromacs Relative Free Energy Calculation Issue On Wed, 5 Oct 2016 09:28:16 +0000 Guanglin Kuang <guang...@kth.se> wrote: > Dear Hannes, > > Part I: > ―――― > I have tried to use FESetup to generate the topology/coordinate files > for the mutated ligands, but I met some problems. Also, I do not recognize anything in your archive file that has been produced by FESetup. -- 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.
