[gmx-users] cyclic peptides

Efi Mantzourani efi_mantz at yahoo.gr
Thu Aug 17 12:12:49 CEST 2006

Hi all,
  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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