AMBER Archive (2004)

Subject: AMBER: How to test the used parameters.

From: tarek mahfouz (
Date: Wed Aug 11 2004 - 11:56:08 CDT

Hello all,
 I have a zinc ion in my pdb file that is non-covalently linked to the
protein. LEaP did not like it to be alone in the pdb file. I created a
frcmod file that had mass and R* and epsilon parameters but still LEaP
was complaining. I had to include it within a HIS residue and create a
" .in" file for the modified HIS residue. I did not want to do this
because I did not want the Zn to be bonded to any residue. LEaP read in
the pdb file this time but when I checked the unit there was missing bond
and angle parameters which I purposly did not add. Anyway, I added
those parameters and when I saved the pdb the zinc was bonded to the 2
histidines. I do not want these bonds, what shall I do? or is it ok to
leave them? Will the deletebond work in this case for further minimization
and MD?
  The other question I have is the parameters I used. I got them from a
reference, how to know they best represent my system? what kind of
tests I need to do?

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