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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Received on Thu May 08 2014 - 09:00:07 PDT
