I am trying to run a gromacs trajectory on a ligand-receptor complex, where the ligand is a head-to-tail cyclic peptide. I add the -ter option in the pdb2gmx command, so that i can turn off the charged termini in the peptide. Unfortunately, it will only work keeping the N terminus as -NH2 (meaning it will add two hydrogens on the resulting structure) or as N (in this case it doesn't add any hydrogens). They are both wrong, as I want one hydrogen, like in a normal peptide bond. If i try to change the resulting files manually its a pain! The gro file is easy enough, but the topology file has to be altered so that the added hydrogen is in the correct atom and residue serial number. That means i have to change all the remaining atoms, all angles, dihedrals etc. Its just impossible as my complex has about 3.000 atoms! Any suggestions???
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