Thank you very much David !
So basically using MMPBSA protocol, it is not possible to calculate
directly the free energy using a simple atom mask corresponding to
chain A and chain B, isn't it ?
Does it mean that in the case when I need to perform mmpbsa analysis I
ought to use an atom mask only based on the residue numbers ?
Many thanks in advance
Enrico
Il giorno mar 4 lug 2023 alle ore 15:47 David Case
<david.case.rutgers.edu> ha scritto:
>
> > Is it possible to retain chain information in the prepared system and
> > store it somewhere in the parmtop file ?
>
> Yes: see the "addpdb" action in parmed.
>
> > If yes, would it be possible to use the atom masks for chains A and B as two selections for
> > subsequent mmgbsa calculations ?
>
> No. The mmpbsa codes don't know how to access and use the "extra" info stored in the prmtop file.
>
> ....dac
>
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Received on Wed Jul 05 2023 - 03:00:02 PDT
