[AMBER] excluding atom sets from MMPB/GB-SA calculations

From: Hallel Freedman <hfreedma.ualberta.ca>
Date: Tue, 16 Dec 2014 17:49:18 -0700

Dear AMBER support,

I was wondering if any of you have any suggestions for me about how to go
about performing an MMGB-SA or MMPB-SA calculation in which contributions
from certain receptor atoms are excluded. In particular I am looking at
the binding of nucleotide analogs and I believe that my results have a lot
of error associated with the high charge in the triphosphate groups; thus
I would like to exclude the atoms in these groups from my calculations.

Thanks,
Holly
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Received on Tue Dec 16 2014 - 17:00:02 PST
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