AMBER Archive (2009)

Subject: RE: [AMBER] Can we use AMBER?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jan 08 2009 - 12:47:18 CST

Hi Richard,

> We would like to run molecular dynamics simulations for the compound shown
> below. Is Amber the correct force field for this? Or are there other
> more appropriate force fields?

You can certainly use it - the Generalized AMBER force field can treat this
type of molecule - The following tutorial explains how to build such a
system: http://ambermd.org/tutorials/basic/tutorial4/

Whether GAFF is the correct force field for this is the million dollar
question. It depends on what you actually want to do and learn.

All the best
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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