[gmx-users] Gromacs Relative Free Energy Calculation Issue

[Hannes Loeffler]

Can you please ask an FESetup specific questions on 
https://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/forum/?action=ForumBrowse&forum_id=1390
otherwise we are going off-topic here.


On Wed, 5 Oct 2016 10:54:25 +0000
Guanglin Kuang <guanglin at kth.se> wrote:

> 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-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf
> Of Hannes Loeffler Sent: Wednesday, October 05, 2016 12:28 PM To:
> gromacs.org_gmx-users at maillist.sys.kth.se Cc: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Gromacs Relative Free Energy Calculation
> Issue
> 
> On Wed, 5 Oct 2016 09:28:16 +0000
> Guanglin Kuang <guanglin at 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-request at gromacs.org.