[gmx-users] disulfide bond
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
Thanks, Peter Nagy
pnagy at utnet.utoledo.edu
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users