From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Oct 02 2007 - 20:16:46 CDT
Sven,
I see what the problem is. You are mutating 4 residues at the same
time, one in each protein segment. The FEP part of Mutator does not
handle this properly, mostly because I didn't expect this kind of
usage, but there is really no reason why it should not be supported.
There is another problem: the code as it is won't generate the correct
behavior for glycine (see "FEP caveats" section in the documentation).
More specifically, the alpha carbon atoms will probably not be tagged
as perturbed.
For now, the workaround is to take the generated PSF, update the
FEPfile "by hand" (quite fast using VMD - make atom selections and use
"set beta 1" or "set beta "-1"), and run alchemify, either standalone
or the version embedded in VMD as a Tcl command.
Jerome
On 10/2/07, SvenBlumenschein_at_gmx.de <SvenBlumenschein_at_gmx.de> wrote:
> Hy
>
> Thanks for the fast replys. Yes I used the psf given by the plugin. Here are the links for my psf and the vmd console output:
>
> http://www.keychem.de/docs/prakt/lys-gly.fep.psf
> http://www.keychem.de/docs/prakt/mutator1.1.log
>
> As you can see alchemify was actually applied.
>
> The angle CT1 C CT2 is not in the parameter file. It is physically not reasonable anyway. How can I prevent or remove these angles?
>
> Thanks in advance Sven
> --
> Psssst! Schon vom neuen GMX MultiMessenger gehört?
> Der kanns mit allen: http://www.gmx.net/de/go/multimessenger
>
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