It would be really helpful if you show the mmpbsa output files where
individual energy terms are listed. It is likely that the covalent terms are
screwed up in the prmtop/inpcrd files that you generated for mmpbsa
calculations.
All the best,
Ray
On Sat, Jan 2, 2010 at 11:43 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com>wrote:
> Hi
> I am going to describe what I have done in detail. I did the MD simulation
> for the complex of protein-protein, subsequently the trajectory file
> (*.mdcrd) was produced, then I used the MM-PBSA in order to calculate the
> binding energy for complex of two proteins. As I mentioned before, I would
> like to determine the effect of important amino acids (in active site) on
> binding affinity, to this end I mutated amino acids to alanine (alanine
> scanning method)in my ligand; *.prmtop and *.inpcrd files for ligand,
> receptor and complex as well as solvated form of complex as implemented in
> tutorial 3 (advanced) were prepared. Then the necessary changes were
> considered in extract_coords.mmpbsa file such as number of atoms (NTOTAL,
> NSTRAT, NSTOP, etc) according to the mutated form of protein. I used the
> following command to obtain snapshots,
>
> $AMBERHOME/exe/mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log
>
> I used the trajectory file of wild type of protein (*.mdcrd). After
> production of snapshots, I used the command shown below for the purpose of
> calculating the binding energy,
> $AMBERHOME/exe/mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>
> But I got the high value for GBTOT and PBTOT, could you please help me in
> this regard,
>
> Thank you in advance,
>
> Maryam
>
>
> --- On Sat, 1/2/10, case <case.biomaps.rutgers.edu> wrote:
>
> > From: case <case.biomaps.rutgers.edu>
> > Subject: Re: [AMBER] problem with MM-PBSA
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Saturday, January 2, 2010, 5:32 PM
> > On Sat, Jan 02, 2010, Maryam Hamzehee
> > wrote:
> > >
> > > In order to save time, I would like to obtain several
> > snapshots of
> > > mutated form of structures from the wild-type
> > trajectory by atomic
> > > coordinate removal and calculate the binding energy
> > so in this way it
> > > is assumed there is no significant structural change
> > upon mutation.
> >
> > > I performed the mutation and calculate the binding
> > energy using the
> > > trajectory of wild type of complex of protein. It was
> > observed that
> > > the values for calculated GBTOT and PBTOT were too
> > high (for example
> > > 2526564) I think there is something wrong with this
> > method,
> >
> > It is safe to assume that something indeed is wrong, but
> > there is too little
> > information given to ascertain the cause. Ignoring
> > structural changes alone
> > would not lead to errors 2 million kcal/mol.
> >
> > ...dac
> >
> >
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> >
>
>
>
>
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Received on Sat Jan 02 2010 - 17:00:02 PST
