Dear Amber User Community,
I am recently running MM/PBSA calculations on a huge protein complex. For
one run, I used the raw trajectories with water/ions stripped. For the
other run, I used trajectories processed with center and image in cpptraj
(no water/ions either). Other settings are identical. From MM/PBSA
calculation results, it seems all the MM components are identical (as I
expected); but the PB part are slightly different. like +- 1 unit on a -200
kcal/mol base.
I am wondering if this means that center-image post-processing on
trajectories would really affect MM/PBSA calculations (I don't think so
tho...) or this slight difference comes from PBSA calculator precision on
floating numbers...?
Thank you for your help and time in advanced! I am not sure if I describe
the question clearly, please let me know if more information would help!
Best,
Guqin
--
Guqin SHI
PhD Candidate in Medicinal Chemistry and Pharmacognosy
College of Pharmacy
The Ohio State University
Columbus, OH, 43210
https://www.linkedin.com/in/guqin-shi-029bb634
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Received on Tue Jul 04 2017 - 06:30:03 PDT
