AMBER Archive (2005)

Subject: Re: AMBER: Formatting Questions

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Feb 22 2005 - 18:03:26 CST

> My ligand is a rather rigid structure.

You might want to look at the porphyrin model. This looks like
info I collated in the mid-90's, perhaps there is something
newer:

  http://www.chem.neu.edu/web/Course/Chm3620/AMBER/Web/ff91_porphyrin.html

It would be interesting to see if the electrostatic/vdw interactions
are sufficient to hold the Ni in place. If not, the choice is between
restraints or an explicit bond. Simple distance restraints could be
convenient in that they would save the trouble of coming up with
angle and torsion parameters, although it might be harder to achieve
rigidity. My guess is that you'd have to create your own nitrogen
atom type if you go the bonding route.

Bill
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