AMBER Archive (2005)

Subject: RE: AMBER: params for cofactors

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Aug 29 2005 - 15:10:55 CDT

Dear Michael,

> I'd like to assemble a collection of cofactors having AMBER atom types
> and charges. Has anyone done a rigorous qm calculation for any of the
> following?:
>
> cAMP, cGMP, porphin, ADP, GDP, ATP<GTP, protophorphyrinIX, heme, NAD,
> NADP, FAD, FADhH, others? Where might parameter sets to use?

Take a look at this website that is referenced from the amber website.

http://pharmacy.man.ac.uk/amber/

It contains a range of different parameter sets included most of those you
mention above along with references to the papers they were published in.

You should also check the $AMBERHOME/dat/contrib directory of an Amber 8
installation.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be ready every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu