My suggestion is that you carefully go over your procedures used to generate
the mutant mdcrd/prmtop files. It has been suggested on the list to do the
suggested file manipulations by hand first before relying on any script. You
can always do some initial consistency check of the files by visualizing in
VMD ...
All the best,
Ray
On Sat, Jan 2, 2010 at 11:24 PM, Maryam Hamzehee <maryam_h_7860.yahoo.com>wrote:
> Dear Lay
> Many thanks for your kind of attention, I performed the calculation for
> wild type as well, here
> is the result,
>
> # DELTA
> # -----------------------
> # MEAN STD
> # =======================
> ELE -463.00 27.67
> VDW -149.13 8.36
> INT 0.00 0.00
> GAS -612.12 25.49
> PBSUR -24.13 0.56
> PBCAL 515.82 23.59
> PBSOL 491.70 23.53
> PBELE 52.83 10.49
> PBTOT -120.42 9.00
> GBSUR -24.13 0.56
> GB 534.30 24.01
> GBSOL 510.17 23.93
> GBELE 71.30 7.70
> GBTOT -101.95 6.41
>
>
> It was good for wild type, another point that I had performed a separate MD
> for mutant form before subsequently the calculation (MM-PBSA) had been done,
> and the result was also good and satisfying. In order to save time and
> according to the paper J Mol Biol (2000) 295: 1-6, I decided to obtain
> snapshots by making the mutant form and calculation of binding energy using
> wild type trajectory(*.mdcrd). So it is assumed that there is no significant
> structural change upon mutation. But there is something wrong in this way!!
>
> All the best,
> Maryam
>
> --- On Sun, 1/3/10, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>
> From: Ray Luo, Ph.D. <ray.luo.uci.edu>
> Subject: Re: [AMBER] problem with MM-PBSA
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Sunday, January 3, 2010, 10:26 AM
>
>
> Your VDW and INT energies are in the tens of millions kcal/mol. So as I
> said, your prmtop/inpcrd files are inconsistent. I assume these runs are
> for
> the mutants. How about your wild type calculations?
>
> All the best,
> Ray
>
> On Sat, Jan 2, 2010 at 10:15 PM, Maryam Hamzehee <maryam_h_7860.yahoo.com
> >wrote:
>
> > Please find the attached output files of MM-PBSA
> >
> > Cheers,
> > Maryam
> >
> > --- On Sun, 1/3/10, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> >
> >
> > From: Ray Luo, Ph.D. <ray.luo.uci.edu>
> > Subject: Re: [AMBER] problem with MM-PBSA
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Date: Sunday, January 3, 2010, 4:09 AM
> >
> >
> > 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 Sun Jan 03 2010 - 17:00:02 PST
