AMBER Archive (2006)

Subject: AMBER: Two different HIS ligands

From: David LeBard (david.lebard_at_asu.edu)
Date: Thu Oct 26 2006 - 16:16:09 CDT

Hi All,

I would like to simulate a system with two HIS ligands that are bound to
a metal atom. Each ligand has slightly different parameters for
equilibrium bond distances to the metal, angle terms between the metal
and HIS atoms, etc. However, I do not exactly know how to change my
frcmod file to account for these two ligands individually.

I have tried simple things like changing the ND1 atom to another type
(ie. from NB to N*), but then I need to introduce back the missing bond
and angle parameters for all atoms touching my new N* atom. What I
would like to do is keep most of the intra-molecular parameters for the
modified HIS residue, but still change the type of the ND1 atom so I can
refer to each ND1 atom explicitly in the frcmod file. What should I be
doing differently?

I believe Ross Walker's tutorial 4 is similar to this situation, however
the frcmod file he gives in the example has the same bond and angle
parameters for the two slightly different HIS ligands.

Thanks in advance,
David

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