[gmx-users] pdb2gmx... cys-cys bonds....
Mark.Abraham at anu.edu.au
Thu Dec 7 12:30:59 CET 2006
> Hello gromacs users,
> I am trying to molecular dynamics simulations on a 30 residues protein.
> I am protonating all the six cysteins after breaking their disulphide
> bonds. This linear non-disulphide bond structure is my starting
> structure for my simulations. After a 5ns dynamics run I would like to
> take the final structure and subsequently form the native bonds again
> and simulate it further for 5 ns. Cys-Cys distances have increased
> considerably after the simulations. I am unable to form the cys-cys
> bonds using the pdb2gmx as the S-S distances are not within the
> disulphide bond range.
There'd be a good reason for this... it would be an unphysically long
bond, and the subsequent dynamics would be weird. If you want to re-form
the bond, do some more MD with a short harmonic restraint between the
two sulfur atoms, and then we they are close enough, alter the topology
in the way you describe.
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