[gmx-users] pdb2gmx not recognizing disulfides

Mark Abraham mark.abraham at anu.edu.au
Mon Jul 2 08:09:59 CEST 2007

>    I did try changing the bond length but it wouldn't catch all the
> disulfides. I do have multiple chains but I don't believe they should be
> merged. My current work around is to just leave the disulfide residues
> named
> CYX according to the amber format and then change them to CYS2 in the .itp
> files for the corresponding .top file. This way pdb2gmx doesn't protonate
> the disulfide residues and the charges for CYS2 are maintained. If anyone
> thinks this is not a good idea, please tell me.

You still won't get them bonded with this procedure... you need a .top
file with S-S bonds, and you get that by producing one by hand or using

If you want pdb2gmx to recognise your S-S bonds, and for some reason which
isn't clear to me, some of thse bonded sulfurs are more than 2A apart,
then you should do a preliminary minimization with constraints on these
S-S pairs to bring them closer together so that pdb2gmx can recognise


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