Hi,
I am interested in calculating DDG for WT - MUTANT of a certain multi peptide system (32 identical peptides). But I cannot use the &alanine_scanning procedure in MMPBSA.py since I need to mutate not one but all 32 residues (one in each peptide) including on the ligand and receptor (31 and 1 peptide respectively). That cannot be done with MMPBSA.py I understand, which allows a single mutation.
So I thought to repeat the whole MD and MMPBSA.py energy calculations, using a 32 ALA mutant receptor, complex and ligand, and then compare the DG of mutant and WT system (using exactly the same conditions).
Is that a reasonable approach?
I mean will I get reasonable DDG (wt - mutants) prediction difference?
Thanks a lot in advance,
Fabian
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
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Received on Thu Oct 29 2015 - 08:30:04 PDT
