[gmx-users] pdb2gmx... cys-cys bonds....

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 7 12:30:59 CET 2006

sharada wrote:
> 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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