AMBER Archive (2004)

Subject: Re: AMBER: Parm98 Vs 02

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Jan 21 2004 - 12:38:31 CST

Dear Madhu,

> Thank you for response.To be precise, in the second chapter for f99
> force field it is given as "changes have been made in many torsional
> parameters" i wanted to know which are those torsional parameters.

- for ff96: the dihedral updates (phi, psi) are for proteins see ref-14 in
amber7.pdf
- for ff98: the dihedral updates (glycosidic linkage) are for nucleic acids see
ref-18 in amber7.pdf

> Further when i looked into the charges, there are notable differences in
> the charge set.for ex in GUA
> N2 -0.923(98) -0.7508(02)
> CA 0.7432(98) 0.6834(02)
>
> How this changes will affect the simulation and is there any test
> run done to check these effects? Thank you very much in advance for any

For the ff94, ff96, ff98 & ff99 the charges have been derived using the 6-31G*
basis set which overestimates the dipolar moment for implicit polarization
simulations (ipol=0 in sander). On the contray, with ff02, the charges have been
derived using B3LYP/cc-pVTZ//HF/6-31g* and the charges obtained are more 'in
vacuo' like and then explicit polarization has to be used (ipol=1 in sander)...

All this is explained in the "Specifying a force field" section of amber7.pdf.

Regards, Francois

F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm

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