AMBER Archive (2008)

Subject: AMBER: N(CN2)- ion

From: babak minoofar (babak_minoofar_at_yahoo.com)
Date: Fri Nov 28 2008 - 07:12:26 CST

Dear Amber users,
  I would like to do some MD simulation of N(CN2)- ion as a counterion of ionic liquid. I have optimized structure from ab initio calculation which looks like the attached pdb file
NCN2_ab_initio.pdb
HETATM 1 C 2 2 0.002 0.000 1.550
HETATM 2 N 2 2 -1.183 0.000 1.721
HETATM 3 N 2 2 1.283 0.000 1.217
HETATM 4 C 2 2 2.195 0.000 2.176
HETATM 5 N 2 2 3.109 0.000 2.947
But after MD pdb looks like this
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 N1 NCN X 2 13.178 16.574 49.431 1.00 0.00
ATOM 2 C1 NCN X 2 12.270 15.908 49.270 1.00 0.00
ATOM 3 N2 NCN X 2 12.032 14.976 50.021 1.00 0.00
ATOM 4 C2 NCN X 2 12.461 13.719 50.326 1.00 0.00
ATOM 5 N3 NCN X 2 13.138 13.152 51.052 1.00 0.00
END
in which the bonds are twisted.
How can I restict the bonds and dihedrals and angles in order to have proper structure.
  Thanks
  Babak

      
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