Joshua Adelman wrote:
> However when I look at the prmtop file that Chamber generates, it fills the TREE_CHAIN_CLASSIFICATION section with BLA (this seems hardcoded in the chamber src), so the above group definitions don't work.
>
> I was wondering if anyone had any suggested work-arounds to this issue? Any ideas would be most appreciated, especially since I'm new to the Amber ecosystem.
Dear Josh,
Yes, this is a shortfall in Chamber; it does not populate
TREE_CHAIN_CLASSIFICATION at all.
I will try, if I get time, to look into this; it may be possible to
implement the algorithm present in tleap's MarkSideChain() and
SetTreeType()functions in:
AmberTools/src/leap/src/leap/unitio.c
using the information present in chamber's bonded_list within the molnt
module.
Regards,
Mark
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Received on Fri Nov 18 2011 - 02:00:02 PST
