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
> _______________________________________________
> AMBER mailing list
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 17 2012 - 06:30:04 PDT
