[gmx-users] Re: Too close water molecules
shakya_79 at yahoo.com
Tue Jan 6 15:37:01 CET 2004
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
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
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
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