Efi Mantzourani wrote:
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???
try making a specbond entry, you have to make sure that the coordinates
are OK. please report back if succesfull.
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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