[gmx-users] SS bond forcing

[Justin A. Lemkul]

Pierre THEVENET wrote:
> 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?
> 

It would be better for you to show us what you tried, along with whatever 
evidence suggests the restraints didn't work.  There are several examples 
provided in the manual, so the only things I would post as examples are already 
available.

-Justin

> 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
>>
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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