[gmx-users] Re: Too close water molecules

[David]

On Tue, 2004-01-06 at 15:51, saurabh shakya wrote:
> Would it be possible to specify the dihedrals
> involving the Fe as improper rather than RB ? would it
> be same ?
Not the same. Maybe you could start by leaving the RB out.
How many are there? At least these:
HB1-CB-SG-FE
HB2-CB-SG-FE
CA-CB-SG-FE

Does the iron have more ligands?
> 
> 
> On Tue, 2004-01-06 at 15:36, saurabh shakya wrote:
> > Making the addition to specbond.dat as you suggested
> > helped to get rid of the extra Hg ,but on running
> > grompp for em i get the following error message 
> > > No default Angle types, using zeroes
> > No default Ryckaert-Bell. types, using zeroes
> > > These messages are for the angles and dihedrals
> > involving Fe . Angle default values and force
> > constants can be given manually but how do I set the
> > RB parameters.
> Not trivial. If you don't have something very similar
> you'll have to
> parameterize the torsion, check the Jorgensen papers
> on the OPLS force
> field. On the other hand, there is probably not much
> happening in that
> region of your molecule, so you could add a RB
> potential that has the
> correct minimum angle. Alternatively you could even
> leave it out.
> > 
> 
> 
> 
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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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