AMBER Archive (2008)

Subject: AMBER: parameters in ff03 and ff99

From: Peter Kiss (
Date: Mon May 19 2008 - 06:21:21 CDT

Dear Amber Developers and Users,
I'm a little bit confused with the paramater development in case of ff99 and
ff03 forcefields.
In case of ff99:
charges: HF/6-31G* geometry optimization, and HF/6-31G* MEp calculations
aminoacid backbone parameters: geometry optimization: HF/6-31G* and electron
correlation energy: MP2/6-31G*.
And what is about the side chain parameters? Were these parameters fitted
based on the small organic molecule dataset results (alkanes,
alkenes,conjugated compounds .. etc)? And which ab initio level was used
(GVB/LMP2 and MP4/TZP, MP2/6-31G*, MP2/6-31G* MP4-BSSE/cc-pVTZ(-f))?
And in case of ff03: charges are: HF/6-31G** structre and MEP: B3LYP/cc-pVTZ
(in ether)?
And in this case only the backbone parameters were fitted, the side chains
were kept from ff99?
I've this question because I have a modified CYS residue, and I would like
to add the missing parameters to the ff03 forcefield.
What I have to do? Geometry optimization at the HF/6-31G* level, relax scan
at the MP2/6-31G*? and the charges should be B3LYP/cc-pVTZ//HF/6-31G**?
Or the charges should be HF/6-31G*//HF/6-31G* because the side chain
parameters were not reparametirzed in the ff03 forcefield?
Thanks in advance,

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