This shouldn't mess anything else up with Amber, as far as I know.
All the best,
Jason
On Fri, Nov 18, 2011 at 8:46 AM, Joshua Adelman <jla65.pitt.edu> wrote:
> > 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Nov 18 2011 - 10:30:06 PST
