[gmx-users] protonated cys -S

[Giacomo Bastianelli]

This is the matrix that I obtain. 

                           CYS1    CYS1    CYS5    CYS5    VAL6   
CYS10   CYS10
                                  N1     SG4     N27    SG30     C38     
N55    SG58
    CYS1     SG4   0.302
    CYS5     N27   0.988   0.900
    CYS5    SG30   1.070   0.917   0.333
    VAL6     C38   1.498   1.396   0.510   0.585
   CYS10     N55   1.122   0.901   0.614   0.609   0.835
   CYS10    SG58   0.879   0.655   0.490   0.422   0.857   0.322
   CYS15     N87   0.784   0.488   1.066   0.984   1.477   0.774   0.620
   CYS15    SG90   0.477   0.202   0.960   0.961   1.432   0.823   0.625
   CYS17    N100   1.030   0.784   0.721   0.460   1.004   0.617   0.387
   CYS17   SG103   1.224   1.039   0.514   0.204   0.625   0.621   0.487
   VAL21    C138   0.756   0.685   0.408   0.388   0.847   0.812   0.531
   CYS22    N140   0.657   0.574   0.404   0.432   0.887   0.742   0.458
   CYS22   SG143   0.755   0.588   0.371   0.430   0.827   0.436   0.203
   VAL29    C196   0.132   0.394   1.117   1.193   1.626   1.248   1.004


                 CYS15   CYS15   CYS17   CYS17   VAL21   CYS22   CYS22
                     N87    SG90    N100   SG103    C138    N140   SG143
   CYS15    SG90   0.320
   CYS17    N100   0.661   0.767
   CYS17   SG103   1.017   1.056   0.412
   VAL21    C138   0.933   0.802   0.602   0.569
   CYS22    N140   0.836   0.686   0.594   0.612   0.133
   CYS22   SG143   0.701   0.606   0.533   0.568   0.419   0.321
   VAL29    C196   0.854   0.555   1.137   1.345   0.869   0.777   0.886

I still have the problem.

The not formed S-S is between CYS1 (first residue of my peptide) and
CYS15. The problem appear only when I add an additional bond between
the N of CYS1 and the C of VAL29 (my last aa) to introduce the cyclic form.
The protonated CYS is number 15.

this is my specbond.dat file:

6
CYS    SG    1    CYS        SG    1    0.2    CYS2    CYS2
CYS    SG    1    HEME    FE    2    0.25    CYS2    HEME
CYS    SG    1    HEME    CAB    1    0.2    CYS2    HEME
CYS    SG    1    HEME    CAC    1    0.2    CYS2    HEME
HIS    NE2    1    HEME    FE    1    0.2    HIS1    HEME
CYS    N      1        VAL    C    1    0.14    CYS2    VAL

when I replace number 6 with 5, the three disulphide bonds are then 
formed well. (??????)

David van der Spoel wrote:
> 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
>>
>
> please check the output of pdb2gmx, in particular the distance matrix, 
> and report it back to the list (completely) if there are problems.
>