[AMBER] Discrepancies in MMPBSA calculations for the same trajectory

From: <Andrew.Warden.csiro.au>
Date: Fri, 25 Aug 2017 04:42:06 +0000


We have performed MMPBSA calculations on a protein/ligand system and various 'resolutions' (ie every 1000 frames, every 100 frame, every frames) and have found that the deltaG numbers do not match up for identical frames. For example, deltaG of -59.345 kcal per mol for frame 8000 in the every-1000-frames MMPBSA calculations, but deltaG of -50.754 kcal per mol for the same frame in the every-frame MMPBSA calculations. No hanges in the mmpbsa.in except for the 'step'

Notably, the overall pattern (rises and falls) of the deltaG's matches up between the different resolutions, it is just the actual numbers that do not.

I was wondering if someone could explain why this might be occurring. I would have thought the numbers should line up exactly for any particular simulation, regardless of the number of frames included (provided the frame number is the same).

Many thanks,

Andrew Warden

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Received on Thu Aug 24 2017 - 22:00:03 PDT
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