[gmx-users] Strange solvation error

[David van der Spoel]

On Mon, 2003-12-01 at 11:48, Raj Badhan wrote:
> Indeed, the dimer is more rectangular in shape.
> But then why is it I can solvate it and EM it without the ATP but 
> when I add the ATP the whole thing doesnt work?
> Would it be worth choosing a different box type?

check the coordinates in your pdb file with a text editor or something
like this. genbox wants to make a box of 7.6 micron for you.


> Many thanks
> > On Mon, 2003-12-01 at 10:55, Raj Badhan wrote:
> > > Dear Anton (and everybody)
> > > My box size is cubic with 0.7 distance between box and molecule.
> > > I can do the same simulation using the dimer in a water box 
> > > without ATP, but when I come to add ATP using the drug-enzyme 
> > > tutorial, this occurs.
> > > I am running this on the windows version, if that helps.
> > 
> > your molecule is very elongated apparently. Or maybe your input pdb file
> > is wrong/unreadable.
> > 
> > 
> > > Any advice would be appreciated.
> > > Many thanks
> > > Raj Badhan
> > > Postgraduate researcher
> > > School of Pharmacy and Pharmacetical Science
> > > The University of Manchester
> > > Manchester, UK.
> > > _______________________________________________
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> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. 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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> 
> 
> Raj Badhan
> Postgraduate researcher
> School of Pharmacy and Pharmacetical Science
> The University of Manchester
> Manchester, UK.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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