Thanks a lot. Yes I got it in manual now :)
..mish
On Thu, May 5, 2011 at 11:31 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> It sounds like you are not setting the receptor and ligand masks correctly
> in the input file. You will have to manually define these variables in the
> MMPBSA.py input file for the ligand and receptor residues you would like
> to
> perform the entropy calculation on.
>
> Good luck!
>
> -Bill
>
> On Thu, May 5, 2011 at 5:25 PM, mish <smncbr.gmail.com> wrote:
>
> > Hello everyone :
> >
> > I have got an issue dealing with Entropy calculation using MM/PBSA.py
> > script. Lets see the problem in this way:
> > I have a system with 6 binding pockets so it has 6 ligands present in it.
> I
> > ran the MD of complex (R+L1+L2+L3+L4+L5+L6) where LI to L6 are the same
> > ligands. Now I am trying to do entropy calculation for each ligand
> (Suppose
> > L1), where rest 5 will be part of receptor. Since, we have to input
> > corresponding prmtop file to generate the snapshots of complex, rec and
> > ligand, the script is generating wrong snapshots. Every time it had the
> > same
> > L6 as Lignad and R+L1-L5 receptor in generated snapshots. I wonder how
> can
> > we deal with this case when same ligand in bound in 6 positions.
> >
> > Thanking U
> > mish
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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>
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Received on Thu May 05 2011 - 15:00:08 PDT
