AMBER Archive (2004)

Subject: RE: AMBER: all_nucleic94 versus all_nucleic02

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Sep 22 2004 - 10:53:49 CDT

Dear Vlad,

> Could somebody explain to me what is the difference between the
> all_nucleic94.lib and all_nucleic02.lib file in the amber library. I
> noticed that the charges on the residues differ.
> Thank you very much

The FF02 force field is designed to be used with dipole polarisability. The
method for calculating the charges within the field created by the
polarisable dipoles is significantly more involved that doing a standard
RESP fit. Details are published but I don't have the details to hand.
Essentially if you are not doing a simulation with polarisation don't use
FF02. Note: FF03 is a standard (non-polarised) force field that also has a
different set of charges, and also some different Phi-Psi dihedral
parameters. The charges in this case were calculated with a continuum
solvent model rather than in gas phase. See the manual for details.

I hope this helps.
All the best
Ross

/\
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|\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 |

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