From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon Oct 01 2007 - 14:47:53 CDT
Hi Sven,
I should add to Chris' reply that normally, Mutator performs the
"alchemify" step automatically. Are you using the PSF file directly as
generated by the plugin? If yes, it would be helpful if you could
provide the output written to the VMD console when running the plugin,
and the resulting hybrid PSF.
Jerome
On 10/1/07, Chris Chipot <Christophe.Chipot_at_edam.uhp-nancy.fr> wrote:
> Sven,
>
>
> what Mutator does is replace an amino-acid residue by an alternate
> one. Combined with the library of dual-topology amino acids, you
> can set up a site-directed mutagenesis experiment, from which a free
> energy difference can be inferred by means of the free energy
> perturbation machinery of NAMD. There is, however, more to it.
> The PSF that you will create contains superfluous terms that ought
> to be removed, namely valence and dihedral angles involving the
> dual side chains. Non-bonded interactions of the latter should
> also be discarded. These post treatment of the PSF can be done
> easily using Jerome Henin's Alchemify code, available on the NAMD
> web page.
>
>
> Chris Chipot
>
>
>
> SvenBlumenschein_at_gmx.de a écrit :
> > Hy NAMD user's
> >
> > I have some trouble getting my FEP startet for my pre-equilibrated system ( potassium channel in a water box, lipids and ions). I mutate a lysine into all other aminoacids in all segments of a potassium channel using the Mutator1.1 in VMD (with 'generate fep file' on). Afterwarts, I try to do a FEP for the diffrent systems. Just to do a test I used the script from the tutorial (A tutorial for alchemical FEP in NAMD). It works when mutating lysine to alanine, but for no other aminoacid - even when lys is mutated to lys itself.
> > The error I get for my Lys-Gly mutant i.e. is:
> >
> > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT1 C CT2
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT1 C CT2
> >
> > Charm++ fatal error:
> > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT1 C CT2
> >
> > or for my Lys-Leu i.e.:
> >
> > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2
> >
> > Charm++ fatal error:
> > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2
> >
> > Can anybody help with some suggestion?
> >
> > 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
>
> E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
> http://www.edam.uhp-nancy.fr
>
> Science without management is worse than management without science
>
> N. G. van Kampen
> _______________________________________________________________________
>
>
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