Thanks for all of your response.
Yes I made the topology files from only backbone and sidechains from .mol2
files .I am exactly not sure how it worked out .
>From the conversations below , only if I somehow have separate residue as
backbone and chains then it will work out to give me the decompostion values
.
Here I will have conflicts in generating partial charges for the part of a
1-mer and I would like to know is it correct to do so.If I consider the
charges as zero and make the structure , will the results for gas phase
energy be meaningful.
Jason you were correct in interpreting my polymer chain .Sorry for not being
so clear in my question.
Thanks
John
On Wed, Nov 24, 2010 at 12:09 AM, Roman Osman <roman.osman.mssm.edu> wrote:
> I just want to make one comment regarding the statement below: MM/
> PBSA is only meant to treat
> >
> > non-covalently bound complexes.
> If that were true decomposition into residue based contributions would
> not be possible because there is a covalent bond between the residues
> in a protein or a DNA. What allows us to do the decomposition is the
> fact that the charges of the residues are zero (or integer positive or
> negative) and that the internal energy is cancelled out. If someone
> can divide the polymer into such units, the decomposition will work.
> After that it's a question of interpretation.
> Best to all the experimenters.
> Rami
>
> On Nov 24, 2010, at 12:02 AM, Jason Swails wrote:
>
> > 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 <s.john634.gmail.com> 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 mmpbsa.pl 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 mm_pbsa.pl
> > 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" MMPBSA.py is "supposed" to be used for that
> > I'm too
> > quick to dismiss the above as impossible without giving it enough
> > critical
> > thought.
> >
> > 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
> > course.
> >
> > Good luck!
> > Jason
> >
> >
> >> Thanks
> >> John
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> Roman Osman
> roman.osman.mssm.edu
>
>
>
>
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>
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Received on Wed Nov 24 2010 - 08:00:03 PST
