AMBER Archive (2007)

Subject: AMBER: Multiple Bonds to one Atom

From: crowfoot_at_unr.nevada.edu
Date: Thu Apr 12 2007 - 15:41:36 CDT

Amber Community,

Using Amber 7, tleap.

We are working on producing gold clusters (~1nm radius) with several (~20-100)
-S-(CH2)n-CH3 chains attached to the gold. To better replicate a cluster, we
have been attempting to create a single BIG gold atom (mass of the cluster, 249
Au atoms; Au-SH bond length of 12.531A; radius of 12.07A).

Currently we are trying to attach 18 thiolate chains to the single BIG gold
atom; however, we receive 12 errors of:

Bond: maximum coordination exceeded on A<Au1 -1>
      -- setting atoms pert=true overrides default limits

(The first six Sulfurs are bound to the Au).

In tleap we have set pert=true for the Au atom, but we receive the same error
when we try to make a bond between any other Sulfur and the Au atom. Does
anyone know of any examples for placing an abnormally high number of bonds
around a single atom?

-Jeremy Crowfoot.
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