I am just getting started with Amber and have recently converted a charmm setup using chamber. During my equilibration protocol, I'd like to first remove positional restraints on the sidechains and then on the backbone. Initially during the heating step, I was just using:
restraintmask=':1-495 & !.H=',
to apply a uniform restraint to all heavy atoms in the protein. Looking at the Amber manual, it appears that the most straightforward way to have different restraints on different groups of atoms is to use the GROUP definitions, and I imagine that you should be able to do something like:
/
Backbone Restraints
5.0
FIND
* * M *
SEARCH
RES 1 495
END
Sidechain Restraints
2.5
FIND
* * S *
* * B *
* * 3 *
SEARCH
RES 1 495
END
END
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.
Thanks,
Josh
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Received on Thu Nov 17 2011 - 11:30:04 PST
