Re: Problems with Mutator1.1, mutations and FEP

From: Chris Chipot (
Date: Tue Oct 02 2007 - 14:42:38 CDT


it is difficult to draw any conclusion from the PSF without seeing
the peptide three-dimensional structure generated by Mutator.

It would also be helpful to have a minimalist PSF, without lipid
and water molecules.

The sequence CT1 C CT2 makes no sense, given the hybrid topology
K2G, i.e. lysine to glycine.

Chris a écrit :
> 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:
> 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


Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Nancy Université Phone: +33 (0)3-83-68-40-97
B.P. 239 Fax: +33 (0)3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex


     Science without management is worse than management without science

                                                        N. G. van Kampen

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