[gmx-users] pdb2gmx not recognizing disulfides

[Mark Abraham]

> Hmm...well the thing is, I just need a .tpr file (which I was getting with
> pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to
> xtc
> format. The simulation is already complete, I'm just converting it, but of
> course the atoms from the tpr need to match those of the trajectory. So
> should I still be doing something different other than my idea to change
> the
> residue names of the .itp files, as mentioned previously? Sorry for some
> of
> my ignorance, I'm still new with much of this. Thanks for all the
> suggestions and input!

So take a frame from the trajectory which you know has sensible disulfide
bond lengths, embed that in a structure file using some Amber tool, and
use that as your input to pdb2gmx.

Mark