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

sharada sharada at ccmb.res.in
Thu Dec 7 13:35:16 CET 2006

Dear  Dr. Mark Abraham,

Thank you for the response. I am into desiging small antibacterial 
peptides with cysteins. I would have to play around with forming 
different combination of disulphide bonds and check the stereochemical 
properties and further design them experimentally to see if they are 
active. I have many peptides  to build models of a lot of  structures 
with different Cys-Cys combinations  for my simulations as my starting 
structures.  If I want to form only those cys-cys pairs then yes I would 
have done the MD with harmonic restraints and bring it near.   I have to 
check  the proximal cys-cys distances and then make a decision on 
building only those disulphide bonds whose S-S distance are  in the 
range of 4A to 5A.    Can I change the pdb2gmx program to make this 
decision?   Is it  possible to change the code?  if so how do I 
incorporate these changes. I think the pdb2gmx program is checking for 
S-S distance to less than or equal to 2A and makes the bond . Am I right 
? Is there a way out in this direction. Kindly help or any other 
suggestion is welcome. Anticipating for a reply.


Mark Abraham wrote:

> 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.
> Mark
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