[gmx-users] pdb2gmx, disulfide bonds and PDB CONECT lines

[Ehud Schreiber]

Dear Gromacs users,

 

I am perturbing a PDB structure in a certain way, and then wish to
obtain a topology for Gromacs minimization, simulation and analysis.
The structure contains some disulfide bonds; however, pdb2gmx guesses
them incorrectly as the distances between the Sulfur atoms change.

Even using the -ss option is not enough, as some bonds are not even
prompted for interactive selection.
The PDB structure contains some CONECT lines specifying the disulfide
bonds, but those are just ignored by pdb2gmx.

 

Can I convince pdb2gmx to use the CONECT lines or in any other way to
create a topology with the desired disulfide bonds?

Preferably the solution should be non-interactive as I handle multiple
perturbed structures.

The perturbations use an existing utility so must be performed on the
PDB level. 

 

Thanks,

Ehud Schreiber.

 

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