AMBER Archive (2007)

Subject: AMBER: AMBER question: Combining Gaff and ff99 forcefields for a single molecule

From: Chris-Kriton Skylaris (C.Skylaris_at_soton.ac.uk)
Date: Fri Feb 23 2007 - 03:54:00 CST

Hello,

I am trying to set up a simulation with AMBER which involves a
DNA segment where one or more of its bases have attached to
them with covalent bonds some organic molecules.
So far I have been able to set up prmtop and inpcrd files for either
the isolated DNA (using ff99) or the isolated organic molecules (using
gaff),
as in the AMBER tutorials, but I can't make xLeap
understand how to bond my organic molecule to a DNA base and
produce prmtop and inpcrd files for the entire system. I would be
obliged if anyone can give me (or point me to) instructions on
how to do this.

With thanks,
Chris

--------- http://www.chem.soton.ac.uk/skylaris.htm ------------
Dr Chris-Kriton Skylaris
Lecturer & Royal Society University Research Fellow
School of Chemistry, University of Southampton, Highfield,
Southampton SO17 1BJ, UK
Tel. +44 (0)2380 599381 (work) +44 (0)7952 650563 (mobile)
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