[gmx-users] to Maik Goette about introduction of ZN in proteins.
grasp2 at mail.ru
Wed Nov 9 17:06:24 CET 2005
thank you for description of ZN-ion introduction in proteins structure:
"I took the mean of the distances in the crystal structure as bond length
and a weak force constant, which I took by intuition...:). I did the
same for the angles. I think, you don't have to care about the
dihedrals...It worked fine with no settings (so GROMACS sets 0s, when I
The charge on the zinc shouldn't be 2, according to severeal papers,
which used that method. with a charge of around .7 it worked fine. Don't
forget to spread the opposing charges equally to the 4 complexing atoms,
to achieve a 0 total charge."
However, I am novice in the molecular dynamics, and I want precise this outline.
Did I understood correctly, that you:
1) introduced several bonds (Zn-ligand) and angles (ligand-zinc-ligand) in ffgmx.itp, where the bonded parameters are listed
2) changed the ZN charge to +0.7
3) introduced a new amino acid CYS-, possessing a negatively charged Sulfur in ffgmx.rtp, the file holding the residue database
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