[gmx-users] Re: gromacs and autodock
magiofer at gmail.com
Mon Jan 9 12:27:58 CET 2006
On 1/9/06, Joanne Hanna <J.F.Hanna at warwick.ac.uk> wrote:
> 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?
Yes, I do. MG
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> 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
> the only format incompatibility I can think of is about residue naming,
> 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
> > > 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
> > > charges or the gmx ff charges for their macromolecule and for
> > > the charges they have derived for their own topologies or the
> > > charges.
> > > I thought it was possibly best to be self consistent and use the
> > > 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
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