From: Jason Swails <>
Date: Wed, 24 Nov 2010 00:02:20 -0500

I'm not exactly sure what you're trying to do, so I'll answer based on how I
interpret your question below:

On Tue, Nov 23, 2010 at 11:26 PM, John S <> wrote:

> Dear Amber User's ,
> I am using mmpbsa- binding energy calculations , for sidechain and
> backbone
> separately with some ligands .
> Sidechains and backbone are built as a single residue with repeating
> polymer
> chain in my sample.In calculations using decomposition of free energy
> contributions , it calculates per residue .Is there any way of specifying
> atom names to find the decomposed values of binding energy.

The decomposition in sander is on a per-residue basis, only, I'm quite sure.

> I tried and made receptor and ligand vacuum topology file with
> only sidechains and only backbone.This conflicts with my original structure
> or the complex.Since the sidechains and backbone are bonded and is it
> proper
> to have topology files of each part of a single molecule.When I run my
> calculations it works out with no error.I am concerned whether this is
> proper or not.

As I understand this: you have 1 system of a repeating polymer unit. Each
unit has what you call a "backbone" and what you call a "sidechain" region.
You've created topology files that have *only* the "backbone" regions and
another topology file that has only the "sidechain" atoms. You are using
these two as your "ligand" and "receptor" prmtops, and completes
with no complaints. I've attempted to depict this pictorially below, where
/\/\ is the backbone and | above it is the sidechain:

   | |
  /\/\ ---> /\/\ + | |

where /\ is bound to the | above covalently (I'm sorry to all those viewing
this with [or without, I suppose] fixed-width fonts that are struggling to
see my vain attempts at chemo-ascii-art)

My response to the above assumption: MM/PBSA is only meant to treat
non-covalently bound complexes, so my instinctual response to the above
setup is that it would definitely not work. However, I'd also expect that
it would be equally unlikely for it to actually complete without error,
assuming you were somehow able to make *correct* topology files of a bare
backbone and floating sidechains. The very idea of those two topology files
seems quite wrong to me, and I think it may turn out to be a bit of a chore
to even create them.

It could also be that I either 1) misinterpreted what you did or 2) I'm too
fixated on what I "know" is "supposed" to be used for that I'm too
quick to dismiss the above as impossible without giving it enough critical

All that said, the approach I described above, if that's indeed what you're
attempting, doesn't make sense to me. Others may comment/correct me, of

Good luck!

> Thanks
> John
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Nov 23 2010 - 21:30:02 PST
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