[gmx-users] SS bond forcing

[Pierre THEVENET]

Thank you for your help, I tried to do as indicated in the link to send 
to me, but it seems that it didn't change anything. Could you show me an 
example, to better understand what I am doing wrong?

Thank you

Pierre THEVENET


Le 06/04/2012 17:19, Justin A. Lemkul a écrit :
>
>
> pithevenet at free.fr wrote:
>> Dear gmx users,
>>
>> I try to use gmx to make some minimization. Unfortunatly, I have some SS
>> bonds which are not formed in my PDB because the S-S atoms are too 
>> far away
>> to connect to each other. I saw at that page :
>> http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds 
>> that it
>> is possible to force GROMACS to make bonds with sulfur atoms by adding a
>> distant constrains between the atoms.
>>
>
> Note that constraints and restraints are different.
>
> http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints 
>
>
>> But I didn't understand in which file it should be inserted and at which
>> step. Can you help me?
>>
>
> If you want to restrain S-S distances to force a more amenable 
> geometry for disulfide formation, what you need are distance 
> restraints in the .top:
>
> http://www.gromacs.org/Documentation/How-tos/Distance_Restraints
>
> Refer to the manual section and figures cited on that page for more 
> information.
>
> -Justin
>