[gmx-users] protonated cys -S

Giacomo Bastianelli gbastian at pasteur.fr
Fri Nov 10 13:29:29 CET 2006

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



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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