AMBER Archive (2009)

Subject: [AMBER] Improper dihedrals between residues?

From: Ben Roberts (roberts_at_qtp.ufl.edu)
Date: Tue Jun 09 2009 - 11:11:15 CDT

Hi all,

I'm trying to specify improper dihedrals in a metal cluster using a
*.prep file. Specifically, I'm wanting to specify impropers between
histidine rings and nickel ions, which are in different residues.

If I try to do so in the IMPROPER section of a given residue's entry
in the *.prep file, leap complains about the nickel ion not existing
in the residue (unsurprisingly). My immediate reaction would be to try
something like "CD2 CE1 NE1 +M" (or "CD2 CE1 NE1 -M"), but I'm told
that +M and -M don't work in position 4 and also that +M and -M are
reserved for the immediately next and immediately previous residue
respectively. The nickel does not come immediately before all
histidines to which it is bound, and while I could re-engineer the
topology to make that so, it would tend to break the rest of the chain.

So, my question is: is it possible to manually specify an improper
dihedral which crosses residue boundaries like this, and if so, how
might I go about doing so?

Thanks,
Ben

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