[gmx-users] Azurin protein attached to metal atom of Cu.

[Alessia Giuliani]

Dear gromacs users,

 I have a problem regarding the simulation of Azurin protein   attached to
metal atom of 
 Cu. I edited the "aminoacids.rtp" file including CU as residue and i added
the type of covalent bond that i need in the terminal part of ffbonded.it
that regard  special bonds.
 I have also added a line to "specbond.dat" regarding the SG-Cu  
 covalent bond. But while running the pdb2gmx command, (without any 
 error) it just adds a SG  with CU  and there is no 
 information on SG-CU bond in topology file. if I include it by hand,
however, is ignored.
 it seems that the program creates a bridge between the atoms but with fixed
distance.
I need a covalent bond to obtained a raman spectrum.

Thanks to all