[gmx-users] Gromacs Relative Free Energy Calculation Issue

[Guanglin Kuang]

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.
--
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