[gmx-users] Re: Too close water molecules
spoel at xray.bmc.uu.se
Tue Jan 6 15:47:01 CET 2004
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.
> On Tue, 2004-01-06 at 11:22, saurabh shakya wrote:
> > The atoms getting close are OW-cys-Hb and the lincs
> > warning almost always occur for Hb .
> > I have a Fe attached to the Sg in my system so I
> > explicitly specified the improper dihedral between
> > Hb-Cb-Sg-Fe and all the other bonds,angles and pairs
> > ,while removing all these parmeters for the Hg as
> > pdb2gmx automatically generates Hg and generates all
> > these values.
> Normally pdb2gmx should make the bond between Cys and
> Fe automatically,
> and there are quite a few extra interactions involved
> How come you have done it manually?
> If your iron is not in a heme environment you may need
> to add lines to
> the file share/top/specbond.dat, like (for bondlength
> of 0.2 nm):
> CYS SG 1 FE FE 1 0.2
> CYS2 FE
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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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