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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