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
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 02 2010 - 23:30:02 PST
