Are you able to visualize the mutated trajectories made by MMPBSA.py using
the mutated prmtop files you created?
On Thu, May 8, 2014 at 12:45 PM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:
> I have already checked. The error is large, and there is a discrepancy
> that I cannot identify in the prmtops themselves. As far as I can tell, all
> is it should be and it should work. What's even more puzzling, is that the
> exact same procedure and method of prmtop generation gives no error
> whatsoever in other residues. Most of the files are simply copy-pasted, and
> I cannot understand why in one case it works and in another it does not.
> Where can I look to see where this difference arises from?
> Pietro
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Bill Miller III
> Sent: 08 May 2014 17:12
> To: AMBER Mailing List
> Subject: Re: [AMBER] Alanine Scanning MMPBSA
>
> In the typical single-trajectory MM-PBSA approach, the bonded terms should
> cancel out exactly when the receptor and ligand energies are subtracted
> from the complex energies. Thus, the delta values for the BOND, ANGLE,
> DIHED, and 1-4 bonded interaction terms should be zero. This error message
> you are seeing is due to one or more of these delta terms being non-zero.
> You should check the values of those terms in your
> FINAL_RESULTS_MMPBSA.dat file for the inconsistencies. If they are
> near-zero, the warning probably just occurred because of a round-off error.
> If they significantly deviate from zero, this may show that you have some
> deeper issues with your prmtop files being incompatible with the mutated
> trajectory.
>
> I hope that helps.
>
> -Bill
>
>
> On Thu, May 8, 2014 at 11:56 AM, Aronica, Pietro <
> pietro.aronica07.imperial.ac.uk> wrote:
>
> > Hello,
> > I'm having problems with MMPBSA. I'm trying to run an Alanine
> > Mutagenesis Scan across a peptide, and it worked fine for the first
> > three residues I tried. On the fourth one, the MMPBSA.out file returns
> > a "INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS" error and
> unusable data.
> > The mutated prmtop was generated in each case by taking the pdb of the
> > original file and manually deleting extraneous atoms to make an
> > alanine out of the original residue. This modified pdb was made into a
> > prmtop using leap, which was then used to make ligand, receptor and
> > complex prmtops with ante-MMPBSA. This process worked fine with the
> > first three mutations I attempted and gave realistic values, but I
> > cannot understand what I did that was wrong in the fourth case. I have
> > diffed all the files involved between working and non-working versions
> and found no relevant differences.
> > What can give rise to the "INCONSISTENCIES" error? Where should I look
> > to troubleshoot this?
> > Cheers
> > Pietro
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Post-doc
> University of Richmond
> 417-549-0952
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>
--
Bill Miller III
Post-doc
University of Richmond
417-549-0952
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Received on Thu May 08 2014 - 10:00:08 PDT
