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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Received on Sat May 17 2014 - 03:30:02 PDT
