[gmx-users] Arbitrary S-S bonds

[rodrid3 at rpi.edu]

What kind of parameters are you using? Gromacs? Amber? I was told you can 
check for previous calculations done for S-S bonds in published papers,
find its constants, bond length, and all and add them to the bonds'
parameter file. 
Then generate a .gro and a .top. It could work. Just make sure you
convert to the appropiate units. 

Good luck.

==============Original message text===============
On Tue, 25 Jul 2006 13:59:14 EDT "Cesar Araujo" wrote:

Hi,

Can anybody tell me how can I generate arbitrary S-S bonds with gromacs?
The problem is that I have a protein and I want to specify some S-S bond
between two cysteine residues but they are not an options given by
pdb2gmx -ss. Should I touch topology file by hand? Why pdb2gmx do not
recognizes automatically SSBOND records in pdb files?

Regards,
César.-===========End of original message text===========