Thanks a lot!
Soumya
On Mon, Sep 17, 2012 at 6:43 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> See my responses to your questions below. I hope they help.
>
> -Bill
>
> On Mon, Sep 17, 2012 at 4:43 AM, Soumya Lipsa Rath
> <soumyalipsabt.gmail.com>wrote:
>
> > Dear Amber Users,
> >
> > I had few queries regarding the results of MMPBSA per residue
> decomposition
> > energy. I define receptor say 1-100, ligand say 200-300. I give the input
> > as follows :
> >
> > &decomp
> > idecomp=1, print_res="41-58;230-300"
> > dec_verbose=1,
> >
> > The tutorial says: "FINAL_DECOMP_MMPBSA.dat output file contains
> > information regarding the interaction of each residue with the rest of
> the
> > system broken down into component parts...".
> >
> > 1. Now the output I get for residue 41 is with respect to the ligand or
> to
> > the receptor or with the residues "230-300" or with the total complex?
> >
>
> The output for residue 41 is the interaction of residue 41 with all of the
> other residues in the total complex.
>
>
> > 2. Is there a way where I can specify residue 41 with respect to a group
> of
> > residues (like giving a mask) and calculate the energy of interaction?
> >
>
> There is no direct way to do this with the code. However, you can calculate
> the pairwise by-residue decomposition for all the residues you are
> interested in. This would give you an interaction energy with residues 41
> and any other residues you specify, although the results are broken down
> per interaction. But that does mean that you could just sum the pairwise
> interactions with residue 41 and any residues you are interested in and
> that should give you the interaction energy between residue 41 and those
> specific residues.
>
>
> >
> >
> > Kindly help me sort out these queries.
> >
> > Thanks
> >
> > Soumya
> > _______________________________________________
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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
> 352-846-1633
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 17 2012 - 07:00:04 PDT
