Subject: Re: [gmx-users] simulating Ubiquitinated protein

[AJIT DATTA]

Thanks David, I could edit the specbond.dat and thus pdb2gmx could make the bond between the desired residues. However, still there are two problems..
1) Once the bond is formed the C-terminal glycine cannot be defined as a terminal one, but pdb2gmx treats it as a terminal residue and thus modifies it to put two oxygens.. Gly-COO- (but this can be taken care of by using -ter card while running pdb2gmx)
However the second one is more problematic..i.e. addition of hydrogen to the modified Lysine residue. I cannot define it to put it in the same plane as NZ, CE and the C from Glycine. Is there anyway to do that?

Thanks

Ajit B.