[gmx-users] protonated cys -S

[David van der Spoel]

Giacomo Bastianelli wrote:
> 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.
>>
> 
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Maybe there is a problem because your are modifying the same residue 
twice. If your peptide is really cyclic you could try to move the final 
VAL residue to be residue 1 (cyclic permutation). Not very elegant but 
it might work.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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