AMBER Archive (2005)

Subject: Re: AMBER: Amber parameters for ADP

From: David A. Case (case_at_scripps.edu)
Date: Sat Jul 30 2005 - 12:08:08 CDT

On Sat, Jul 30, 2005, zgleo wrote:

> Has anybody used the ADP parameters of Carlson
> (http://pharmacy.man.ac.uk/amber/)? I found that the topology of the
> molecule is not correct while viewing in xLeap. I don't know if this is
> relevant for the use of the parameter. Can anyone give some idea?

The topology (bond connectivity looks fine. The O3B atom seems to be located
in a bad place. This would not be a problem if (as is most common) you load
the coordinates from a pdb file. But it probably should be fixed so that the
file can be used for model building as well.

...dac

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