Dear Alan,
Please look in the amber tools manual. Every file is well described
there. The archive of the list has also a massive number of discussions
about different ff variants. Currently, the recommended ff variant for
proteins is ff99SB while for nucleic acids ff99bsc0 (check the original
references to understand the modifications introduced in these variants
comparing to ff99 and how they improved the behavior of biomolecules in
MD simulations). There are also other variants included with the amber
distribution that are worth considering (such as ff03 - this variant
implements a completely different charge derivation scheme for amino
acids comparing to all ff99 variants -). My advice is to take some time
to understand these ff variants before deciding on one or the other.
Following closely the previous discussions as well as reading the papers
describing each variant should proceed any calculations.
Vlad
Alan wrote:
> Hi List!
>
> This file amber10/dat/leap/cmd/README need some update. For
> example leaprc.ff99 is in oldff dir for amberTools 1.0.
>
> I am playing with antechamber and tleap. May someone tell me which
> file better replace leaprc.ff99? leaprc.ff03? What are leaprc.ff99SB
> and leaprc.ff99bsc0?
>
> Many thanks in advance.
>
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
--
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Dr. Vlad Cojocaru
EML Research gGmbH
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Tel: ++49-6221-533266
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Wed Jun 25 2008 - 06:07:27 PDT
