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Hello Yi--
> Thank you for the previous replies. I now need to confirm the allowed
> space for MTSL side chain to move freely. In the other words, after
> calculated structure with NOE restraints, I substitute a specific
> residue to CYSP with addatoms.py. Since the generated structure might
> not be at its lowest energy state and the MTSL side chain could sample
> a large space, I am thinking about doing energy minimization with
> fixed backbone atoms. The process should be similar with the
> preminimization step in AMBER. Which script should I use? Or can I
> just comment out the restraints and heat-cooling part of the original
> 'anneal.py' script, then fix the backbone atoms?
You can use a simplified version of the script, where you fix sidechains
you're not interesting in using something like
backbone="name CA or name N or name C or name O or name HN or name HA"
dyn.fix("(%s) and not resid 53 and not resname TAU" % backbone)
>
> Also, is there a simple way to convert MTSL or CYSP parameters (topology,
> bond, charge, etc.) to AMBER?
>
I don't know how to do this, but I'm sure it's not too hard. Note,
however, that Xplor-NIH force constants usually are not appropriate for
general MD calculations.
best regards--
Charles
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