AMBER Archive (2004)

Subject: RE: AMBER: parameter development for nucleotide analogues

From: Ross Walker (
Date: Thu Jul 08 2004 - 12:49:33 CDT

Dear Vlad,

> I have developed new parameters for several fluorescent
> base analogues
> for incorporating them into RNA. I would like to publish the
> results and
> I was wondering how could one prove that the parameters are
> performing
> well. From your own experience could you indicate me what kind of
> calculations could one perform in order to show that these
> parameters
> perform well. They were developed by analogy with gaff force
> field and
> the charges were calculated with RESP as described for Amber
> (Gaussian +
> RSEP) using a methyl group instead of sugar.
> Thank you very much for any kind of suggestions

Typically people do comparissons between predicted structures from the
classical simulations and experiment or high level ab initio data. Comparing
things like predicted bond lengths, angles and energies for certain
rotations etc. You should also look at predicted vibrational frequencies
(nmode) and compare these to experiment and ab initio data. If you want to
stay consistent with Amber you should take a look at the various papers
referenced for the parameters in the parm files. E.g parm99.dat. From these
papers you'll find examples of how each of the specified parameters was

I hope this helps
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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