Hello All
I have four protein-DNA complexes first is wt, second DNA mutant, third protein
mutant and fourth both mutant. I have to calculate binding free energy of these
complexes.
When I ran MD simulation of all these and calculate binding free energy, I got
binding free energy as follows:
First MD
wt = -77.4 kcal/mol
DNA mutant = -59.7 kcal/mol
protein mutant = -77.2 kcal/mol
both mutant = -73.9 kcal/mol
Second MD run
wt = -72.9 kcal/mol
DNA mutant = -91 kcal/mol
protein mutant = -74 kcal/mol
both mutant = -86.8 kcal/mol
Is it possible to reproduce the result? I also claulated residue wise energy
decomposition there also I am getting diffrent result residue which is not
involve in interaction energy of that residue in first MD run is unfavorable
(2.9 kcal/mol) but in second MD run become favorable (-10.7 kcal/mol). So I am
not able to justify my result.
Is here my approach to claulate bindng free energy is correct, i.e. run two MD
simulation and then calculation of binding free energy is correct so that I can
also calculate STD of two result or run MMPBSA two times of a single MD run and
calculate STD of two MMPBSA calculation ?
Can anybody please suggest me
With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
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सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
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Received on Mon Jun 11 2012 - 02:30:02 PDT
