> 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
>
Hi Mark,
Thanks for your response. I was wondering if I were to just write a script to replace the TREE_CHAIN_CLASSIFICATION section in the script with some approximation of the correct labeling (perhaps just marking residues as M or S and then leaving everything else the same as chamber originally wrote it) for the purposes of setting restraints, would this mess anything else up with Amber? In other words, does this information get used elsewhere by Sander such that marking something incorrectly as S, when it should be 3, would effect the correctness of the dynamics?
Thanks,
Josh
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Received on Fri Nov 18 2011 - 06:00:09 PST
