[gmx-users] Re: gromacs and autodock

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 9 09:21:56 CET 2006

Joanne Hanna wrote:
> Hi
> I was wondering whether anyone on the list has experience using gromacs
> output (with polar Hs) in autodock, as I am struggling with some kind of
> seemingly random file format incompatibility.
> I was also wondering whether when using autodock people use the kollman
> charges or the gmx ff charges for their macromolecule and for ligands
> the charges they have derived for their own topologies or the gasteiger
> charges. 
> I thought it was possibly best to be self consistent and use the same
> charges that I have used for docking as I have and will in MD
> simulations.
> Sorry its a bit of a waffley question.

You should probably use charges that Autodock usually uses, since it 
also has its own LJ parameters.

> Hope someone can help
> 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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