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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>
--
Bill Miller III
Post-doc
University of Richmond
417-549-0952
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Received on Thu May 08 2014 - 09:30:04 PDT
