[gmx-users] Re: gromacs and autodock

[Joanne Hanna]

Hi  

Yes that might be the source of my problem I have not checked this.
Thanks for the suggestion. 
When you use autodock do you use the kollman charges and gasteiger
charges for ligands?


Thanks 
Jo

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

J.F.Hanna at warwick.ac.uk
>>> magiofer at gmail.com 01/09/06 10:26 AM >>>
Hi Jo,
well, I used to employ both GROMACS and AutoDock on my systems, but
usually
the only format incompatibility I can think of is about residue naming,
for
instance I used HISA and HISB, LYSH and CYSH protonation, they should be
renamed (without changing protonation of course) to HIS, LYS and CYS.
Besides, if you have aromatic carbons in your ligand, you should change
their atom types from C to A, using the AutoDock function in the Ligand
menu.
That's all I think.
I hope it helps.
MG

On 1/9/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> 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.
>
________________________________________________________________________
> 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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