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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