[gmx-users] Problems with undefined Bond types, angles and dihedrals

[Mr.Sridhar]

ear GMX users,

Iam doing MD on a protein containing heme cofactor.  But some
of the bond types, bond angles and dihedral angles in the heme are not
getting recognised. The folowing warnings were displayed.

#########################################
No default G96Bond types, using zeroes.
No default G96Angle types, using zeroes.
No default Proper Dih. types, using zeroes.
###########################################

The bond type that is not recognised was between SG of CYS in protein  and
FE of HEME.
The angle types that were not recognised were between SG-FE-NR; SG of CYS
FE and NR of HEME.
The dihedral type that were not recognised was between CH1-CH2-SG-FE ;
CH1, CH2 of CYS and FE of HEME

The dynamics ran succesfully, but I doubt this usage of zeroes for these
types would affect correct running of Simulation.

I'll be very grateful to you if you suggest me how to overcome this
problem.


Thank you.

sridhar