From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Mon Oct 01 2007 - 13:57:58 CDT
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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