[AMBER] MMGBSA giving to high VDW energies

From: Ahmed Ayoub <atayoub.ualberta.ca>
Date: Fri, 5 Sep 2014 13:12:00 -0600

Dear Amber users,

I'm calculating the MMGBSA binding energies (with per-residue
decomposition) between two protein subunits) when I check the intermediate
files (_MMPBSA_complex_gb.mdout.X) I see a weird behavior. All residues
belonging to the 1st subunit (except last three residues) have normal
energies while the last three residues in the first subunit as well as the
all second subunit residues have unusual vdW energies that sometimes reach
I have checked the structure and specially the problematic residues and
they seem to be fine with no abnormal clashes!
Also, the job crashes after a while complaining about memory.
Any help?

Ahmed Taha Ayoub
PhD Candidate, Theoretical and Computational Chemistry
W4-54, Department of Chemistry
11227 Saskatchewan Drive
University of Alberta
Edmonton, Alberta T6G 2G2
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Received on Fri Sep 05 2014 - 12:30:02 PDT
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