Le 13/02/13 14:55, Miguel Ortiz Lombardía a écrit :
>
> Hi,
>
> I have a question concerning the value of the sasopt option when using
> pbsa for PB analysis within MMPBSA.py in the case one uses inp=1. If I
> understand correctly, inp=1 implies use_sav=0. In this case there is no
> dispersive component in the non-polar part, and the cavity energy is
> calculated from the area of the solvent accessible surface (SAS) with
> cavity= a*SASA + b.
>
> Now, I see in the manual that pbsa uses sasopt to control the type of
> molecular surface that is calculated. The default is saspot=0 wich
> calculates the solvent excluded surface (SES). SES is sensibly smaller
> than SAS, so I thought that using inp=1 I should use sasopt=1 to require
> SAS calculation.
>
Partly answering myself here:
I calculated with Chimera the SAS and SES of a few of the snapshots in
the trajectories and compared them to the ones reported by pbsa when I
do NOT set sasopt. It seems that even when I don't set sasopt the
surface reported does correspond to SAS. Thus, my interpretation of what
sasopt does was not correct. I guess sasopt is not used in the non-polar
part of the calculations and setting it to 1 may break other things.
Yet, if someone wants to comment on my input files, I'll be glad to
listen to what more experienced people can say.
Thank you and sorry if I wasted some of your time.
Cheers,
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Wed Feb 13 2013 - 06:30:02 PST
