[gmx-users] bond stability during minimization

[Mustafa Toprakçý]

Dear Gromacs Users,
I have completed an energy minimzation on an enzyme-ligand complex. 
Everything is fine but when I inspect the resultant structure I see
a bond in the co-factor FAD is broken. This occurs repeatedly and 
regardless of the type of EM algorithm. 
  The bonds is between C10 and N1 of FAD structure of the enzyme. 
I inspected the bond parameters in the topology file and it is

atoms    type  b0        Fc
NR6  CB  1     0.13400   418400.00

I have sent the FAD molecule to PRODRG and got the same parameters
for this bond. I have also investigated other force field parameters
and they have got the same length and similar force constant. 
 This bond occurs in several places in FAD molecule. But only the 
one which is in the catalytic site gets broken.
 I will be glad if you help me deal with this problem. I think this
may cause problem when I use this structue in MD. I think that I may
increase the force constant in the parameter file or another type of
bond fuction for these two atom. Can I use these and how?

Regards,
Mustafa Toprakçý


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