AMBER: Atoms overlapping

From: Nitin Bhardwaj <>
Date: Mon, 11 Dec 2006 13:43:44 -0600

Dear Amber users,
  I am having a strange problem during my simultion. For one of my lipids, I
have a hydrogen (say H1) connected to an Oxygen (say O1). O1 is in turn
connected to Phosphorus (P). Also connected to P is another oxygen (say O2)
that is negatively charged. Picture is sthg like this:

Now if I use amber atomtype (instead of gaff), in the first step of
minimization itself, H1 almost overlaps with O2 (distance being 0.001 Ang)
while still being bonded to O1. I checked the parameters:

H1 is atomtype 'ho' (charge 0.4233), O1 is 'oh' (charge -0.7908) and O2 is
'o' (charge -0.8586).

Also, the charges written in the prmtop file for all these atoms are
different (they are, respectively,
7.71386404E+00 -1.44094659E+01 -1.56451201E+01).

What could be going wrong?

Thanks a lot for your help in advance.

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Received on Wed Dec 13 2006 - 05:21:44 PST
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