[gmx-users] protonated cys -S

[Maik Goette]

Try renaming the Cys in the the PDB to CYS2.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Giacomo Bastianelli wrote:
> Hi Tsjerk,
> 
> the distance of the "not formed" S-S is 0.202
> while the two "formed" S-S are 0.204 and 0.203.
> Therefore, gromacs should recognize all three and
> create the SS bonds.
> 
> CYS    SG    1    CYS    SG    1    0.2    CYS2    CYS2
> 
> this is the second line of my specbond.dat
> 
> Thanks,
> 
> Giacomo
> 
> Tsjerk Wassenaar wrote:
>> Hi Giacomo,
>>
>> The two sulphur atoms have to be at a proper distance to be recognized
>> as involved in a S-S bond. In your case, if you're certain that there
>> should be a bond, you have to edit the file specbond.dat, find the
>> entry which links two cysteine residues and set the distance to the
>> actual distance in your structure (there is a 10% margin).
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On 11/10/06, Giacomo Bastianelli <gbastian at pasteur.fr> wrote:
>>> Dear users,
>>>
>>> I have just found that gromacs protonate the -S of
>>> my Cys and I would like to have it deprotonated
>>> to form a disulphide bond (It is present in the original
>>> pdb file).
>>>
>>> Is there any way I can modify it?
>>>
>>> thanks in advance,
>>>
>>> Giacomo
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>>
>>
> 
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