Dear all,
I am using amber12 with the ff12SB force field. I would like to
post-process MD trajectories
(for binding energy calculations) using mm_pbsa, but it seems that the
newer atom types of the ff12SB force field have not been incorporated
into
pbsa (PB Bomb in pb_aaradi(): No radius assigned for atom....etc etc).
I have seen plenty of discussion about this issue in the amber mailing
list.
Unfortunately, editing the topology files with xparmed when huge
numbers of mm_pbsa runs are planned is not such a straightforward
solution....
therefore may I ask if there is anybody so kind to provide some basic
instructions on where to define such atom types in the pbsa source
code.
I think that would be of great help.
Thank you very much in advance for your help.
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Received on Tue Jan 15 2013 - 08:30:02 PST
