[gmx-users] partial charges

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 5 09:04:57 CEST 2005

On Mon, 2005-09-05 at 01:18 +0100, Joanne Hanna wrote:
> Hi
> I was wodnering how the partial charges for ligands in the ffG43a2.rtp files were calculated, more specifically the ATP molecule.
> I have calculated (fitted) charges for an AMP molecule using gaussian and 6-31g basis sets, however these charges are quite drastically different to the ATP charges, particularly on the adenine ring.
> Also on an unrelated matter and probably a very trivial question but if i was wanting to use position restraints on atoms of 10 Kj/mol, in the posre.itp file this would correspond to values of 10 in each of the x y and z direction for each atom? is this correct?
check recent gromos papers, you will probably find that the charges were
determined empirically . that doesn't matter if they give the right
> Many thanks
> Jo
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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