AMBER Archive (2009)

Subject: RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane

From: intra\\sa175950 (stephane.abel_at_cea.fr)
Date: Fri Dec 04 2009 - 03:54:55 CST

Thank you Ross and Francois for your explanations and references

My question came because I have done some MD with the CHARMM (Klauda et al.)
and GLYCAM06 ff and I would like to explain in my paper why I found some a
slight difference (~12%, GLYCAM06=84% and CHARMM=72%) in the average trans
population for the CCCC angles in the alkyl chain between these two ff.
Since these results are similar that others ones obtained in my lab with the
FF99SB parameters, I am not worried about this result.

For FyD, PM: I will contact you shortly with a first draft of the paper.

Stéphane

-----Message d'origine-----
De : amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] De la part
de Ross Walker
Envoyé : jeudi 3 décembre 2009 18:53
À : 'AMBER Mailing List'
Objet : RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane

Hi Stephane,

> Does anybody know some MD papers/refences where the CHARMM and AMBER ff
> are
> compared especially when they are used for simulations of long alkane
> (n <
> 4).

I do not know of any papers specifically comparing alkanes, others may know
of some. You should note that the AMBER and CHARMM force fields were largely
designed for proteins and so long alkanes fall outside of their design
specs. However, you can look up the parameters fairly easily.

In AMBER FF99SB the atom types would be as follows:

     HC
     |
CT---CT---
     |
     HC

CT-HC 340.0 1.090
CT-CT 310.0 1.526
CT-CT-HC 50.0 109.50
CT-CT-CT 40.0 109.50
HC-CT-HC 35.0 109.50
X -CT-CT-X 9 1.40 0.0 3.

In Charmm all22 this would be

    HA
    |
 ---CT2---
    |
    HA

With CT3 for the ending methyl groups.

CT2 CT2 222.500 1.5300
HA CT2 309.000 1.1110
CT2 CT2 CT2 58.350 113.60 11.16 2.56100
HA CT2 HA 35.500 109.00 5.40 1.80200
HA CT2 CT2 26.500 110.10 22.53 2.17900
X CT2 CT2 X 0.1950 3 0.00

Hence here are some fairly large differences in the covalent parameters. The
charges will also of course be different but this will depend on the
specific alkane. Charmm always sums methyl groups to zero charge while AMBER
sums the whole molecule to zero.

The actual affect that these parameter difference have on the underlying
dynamics I do not know but you could probably devise some fairly simple test
runs to study this.

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |

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