AMBER: GAFF + AM1BCC & small-molecule aggregation

From: Scott P Brown <>
Date: Wed, 1 Mar 2006 14:00:33 -0600

Dear AMBER Community,

I've run a Langevin dynamics simulation of a system composed of the
protein bcl solvated in explicit water containing a number of
adenosine-like small molecules. After a nanosecond of so of production
dynamics the adenosine compounds have begun to aggregate into rather large
clusters. This aggregation behavior was not expected (at least not by
me). The adenosine molecules have been parameterized using GAFF with
AM1-BCC partial charges, and the protein is using ff03 with TIP3 waters.

What I'm wondering is if anyone out there has any experience with GAFF &
AM1-BCC under these conditions.. is it to be expected (i.e. not
surprising) that GAFF & AM1-BCC produce unrealistic force-field/charge
assignments for small molecules under these conditions?

In case anyone is interested in taking a look.. I'm attaching a PDB
snapshot of the system, along with the SANDER input file and a MOL2 file
showing the Antechamber GAFF atom assignments & AM1-BCC partial changes.

Thanks for any insight you may have..


Scott P Brown, PhD
Senior R&D Computational Scientist
Dept R42T / Bldg AP10-LL
100 Abbott Park Rd
Abbott Park, IL 60064-6115
Tel: (847) 937-1996
Fax: (847) 938-2478

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Received on Sun Mar 05 2006 - 06:10:13 PST
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