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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Received on Sat Jan 02 2010 - 12:00:03 PST
