[gmx-users] Cys-Cys Bond

fulya caglar fulyacaglar at yahoo.com
Mon May 7 21:03:02 CEST 2007

Hi everone.
  I'm studying on a protein including two chains with four disulfide bonds.when I
watched the simulation I saw that A and B chains were splitting from
eachother.Then I gave that command.
   pdb2gmx    -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro  -merge  -ss  -inter   -ignh.
  But the chains split from eachother again.In specbond.dat only one CYS-CYS bond appears.Should I  add three more lines to the file like this?
  CYS  SG   1     CYS    SG    1   0.2   CYS2   CYS2

  What can I do to identify the  -SS bond other than these?
  Thank you
  Best regards
  Fulya Caglar
  Hacettepe  University

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