[AMBER] MMPBSA calculations

From: Baptiste Legrand <bap.legrand.gmail.com>
Date: Thu, 6 Feb 2020 12:14:17 +0100

Hi all,

I just finished the tutorial about the MM/PB(GB)SA method with my
complex. All is fine and using cuda, after some optimizations, the
calculations could be launched on a workstation. I have just few general
questions, reading the literature, one can found for similar complexes
very different lengths of production run, from few ns to 1000 ns. I
imagine that the error decrease with the length of the run and the
number of frames but are there general/reasonable parameters? or each
user should test different length of MD production before incorporating
mutations etc.?

Also, I found the tutorial to decompose the free energy contributions of
each residue (quite redundant with the ala-scan?), but it seems to be
appropriate only for amber11?



Best regards,


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Received on Thu Feb 06 2020 - 03:30:02 PST
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