Hello all:
I am running MM/PBSA on a homodimer that has three disulfide bonds in each monomer and one disulfide bridge between the monomer. I created the gas-phase topology files for two monomers (that are same since it is homodimer) and complex using tleap.
Since original solvated complex has disulfide bonds explicitly defined (seven total), I used the same information to create gas-phase topologies. The MMPBSA calculation ran fine but with the following error:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
If I remove the disulfide bridge information in the leap input file and create the gas-phase topology files, the above WARNING goes away, but the DeltaG values are very high.
Also, if I run PBSA calculation on one frame, the bond/angle/dihedral shows non-zero values if I use Disulfide bond but they are zero if I do not use disulfide bond in gas-phase topology files. The solvated simulation was run for 200 ns in water and did have disulfide bonds explicitly defined in solvated topology files (obviously).
Am I doing something wrong here? Or one should not use disulfide links in the gas-phase topology?
I am using AMBER12 and using MPI version of MMPBSA.
Thanks for your help
Divi
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Received on Tue Jan 15 2013 - 11:30:04 PST
