[gmx-users] disulfide bond

Nagy, Peter I. PNAGY at UTNet.UToledo.Edu
Sat Aug 2 01:52:00 CEST 2003

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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