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

sharada sharada at ccmb.res.in
Thu Dec 7 06:50:44 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.  I have gone through the gmx_users archives and 
found that one can do by changing specbond.dat file.  What exactly I 
have to change there so that pdb2gmx forms the cys-cys bonds. Can  I 
override this and ask it to form the disulphide bonds any way.  Is there 
any other way one could force  cysteins to form disulphide bonds ?  I am 
sure there must be a way .  Any suggestions or  ideas. Thanks a ton in 


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