[gmx-users] disulfide bond

Marc Ceruso mceruso at physbio.mssm.edu
Sat Aug 2 01:57:01 CEST 2003

disulfide bondTry renaming CYX to CYS, pdb2gmx should find the disulfide bond by itself.

  ----- Original Message ----- 
  From: Nagy, Peter I. 
  To: gmx-users at gromacs.org 
  Sent: Friday, August 01, 2003 7:51 PM
  Subject: [gmx-users] disulfide bond

  Dear Gromacs Users!

     I created a pdb file for a protein in Sybyl, where I had a disulfide bond.
  Sybyl distinguished these two residues by CYX as compared to the regular CYS.
     When I used pdb2gmx, the system complained about CYX and responded that
  tries to consider these residues as CYS2. It was fine, but in the conf.gro and topol.top files I noticed that the backbone H (to N) was not generated.
  Furthermore, the S-S bond was not generated in the topol.top file.
     Perhaps I could edit this latter file by following the topology and charge
  parameters for a backbone H(N), but I do not have its coordinates in the conf.gro. I am sure that there is a simple way to handle the S-S in Gromacs.
     What should I modify in the original .pdf file to get correct .gro and
  .top files?

  Thanks, Peter Nagy
  pnagy at utnet.utoledo.edu 
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