[gmx-users] Re: Too close water molecules

saurabh shakya 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
RB parameters.


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

Do you Yahoo!?
Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes

More information about the gromacs.org_gmx-users mailing list