Hi Bill, I have related questions regarding MMPBSA per residue analysis, and I'm slightly confused.I've done MMPBSA per residue decomposition for system composed of a peptide (treated as the ligand) and a membrane monolayer (treated as the receptor), disregarding the entropy changes. I initially planned to show, in a table, the total contribution to the binding enthalpy made by the peptide and the monolayer, respectively. By summing the decomposition energiesin each case. When the output for one residue is the energy resulting from its interaction with all the other residues in the system, am I not summing a given interaction energy several times? And if so, why is deltaG(peptide) + deltaG(monolayer) + deltaG(non-polar) = deltaG(total)? Thanks in advance. Best regards, Åge Aleksander SkjevikDepartment of BiomedicineUniversity of Bergen, Norway > Date: Mon, 17 Sep 2012 09:13:16 -0400
> From: brmilleriii.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] MMPBSA per-residue
>
> 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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> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-846-1633
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Received on Thu Sep 20 2012 - 08:30:03 PDT
