[gmx-users] Strange problem with simple FEP (bug?)

Maik Goette mgoette at mpi-bpc.mpg.de
Tue Nov 7 14:48:39 CET 2006


Checked it with the Amber99 port. Same strange habit. It occured with 
another protein (system), too.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Maik Goette wrote:
> Hey all
> I'm trying to do a simple FEP within a simple protein, which seems to 
> make things simple...but as you may expect...it is anything else than that.
> What I'm trying to do is morphing a Tyrosine into a Phenylalanine in 
> Therefore the CZ is changed from the type of TYR to the type of PHE.
> The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a 
> dummy (PHE). So this is very simple. We checked the tpr-dump and 
> everything looks fine (except, maybe, we missed it). Now, in the 
> position-restraint run (where state B should not be regarded by the 
> system), the OH-proton moves on top of the OH-oxygen and the simulation 
> crashes after a while. We then performed a FEP from TYR to TYR (so A- 
> and B-state are the same) and the system runs.
> The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions?
> Gerrit and me think of a bug somewhere.
> Regards

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