[gmx-users] AMBER99sb-ILDN charges for C-terminus GLY with COOH capping

[santanu roy]

Hello all,

I am using pdb2gmx (4.5.5 version) to create an AMBER99sb-ILDN topology
file for a peptide. It gives me only NH3+ as the N-terminus and COO- as the
C-terminus. But, I want to have the C-terminus as COOH. The C-terminal
residue is GLY.

Can anybody give me some idea how to get the GLY COOH C-terminus using this
force-field? What could be the charges for the terminus?

Thanks a lot,
Santanu