Thanks for your replies.
When I use the topology files generated by ant-MMPBSA.py I encounter the
following error
"Error: Atom mismatch in your prmtop files! Complex natom != Receptor natom
+ Ligand natom."
The most likely reason being the terminal residues. In my case I am trying
to find the binding energy of a portion of the complex (which lies at
the center) with the remaining protein, but generally when we calculate the
binding energy of the ligand molecule it generally lies at the end of the
complex.
Can I get some suggestion on how to approach this problem?
Thanks,
Soumya
On Sat, May 17, 2014 at 6:18 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Hii;
>
> I would suggest check the topology and co-ordinate files and run 5
> different md with different initial velocities and compute binding free
> energy from each trajectory and check the trend. I think if u use the
> original co-ordinates and check the trend you might be sure that binding
> free energies are convenient. Though MM based bindingfree energy are very
> artifacts still if you adapt multiple trajectory approach and check the
> trend it might be convenient. Better way of testing is test the difference
> in binding free energy by taking one wild and one mutant as starting
> conformation and monitor the difference based on multiple md trajectories.
>
>
> On Sat, May 17, 2014 at 1:11 PM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > As the warning message suggests, there appears to be some inconsistencies
> > among your topology files. I am not sure how you made your individual
> > prmtop files, but I would suggest remaking them using the ante-MMPBSA.py
> > program in Amber. This allows you to input the solvated complex topology
> > file and write out the dry complex, receptor, and ligand prmtop files
> based
> > on the original. This should prevent any inconsistencies between the
> > different files.
> >
> > Good luck!
> >
> > -Bill
> >
> > On May 17, 2014, at 6:04 AM, Soumya Lipsa Rath <soumyalipsabt.gmail.com>
> > wrote:
> >
> > > Dear Amber Users,
> > >
> > > I am trying to calculate MMPBSA for few residues of Protein B to the
> > total
> > > complex of ProteinA/ProteinB. I generated the individual topology files
> > and
> > > calculated the energies. However, the MMPB/GBSA results file shows the
> > > following warning
> > > "GENERALIZED BORN:
> > >
> > > WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND,
> > > ANGLE, AND/OR DIHED).
> > > CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT
> BE
> > > RELIABLE (check differences)!
> > >
> > > WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
> > > CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT
> BE
> > > RELIABLE (check differences)!
> > >
> > > The most common cause of this is inconsistent charge definitions across
> > > topology files."
> > >
> > > Along with that, I get an additional 1-4 VDW and 1-4 EEL values
> along
> > > with conventional bond, angle, dihedral, VDWAALS, EEL, EGB, ESURF, G
> gas
> > > and G solv in the results file. When I try to find the binding energy
> of
> > > proteinA with proteinB I don't encounter such warnings.
> > >
> > > I have made sure the total number of atoms are same, however, I keep
> > > getting this warning. I have checked the pdb files and topology files
> as
> > > well but I am unable to locate where the error lies. Can anybody please
> > > suggest me where I might have gone wrong?
> > >
> > > Thanks,
> > >
> > > Soumya
> > > _______________________________________________
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> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
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>
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Received on Sun May 18 2014 - 22:30:02 PDT
