[gmx-users] Re: gromacs and autodock
magiofer at gmail.com
Mon Jan 9 10:59:26 CET 2006
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
That's all I think.
I hope it helps.
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 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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