[gmx-users] inter-chain disulfide bridges

[HERNANDEZ ALBA Oscar (IPHC)]

Hello everyone,



     I have a problem related with a molecule with inter- and intra-chain
disulfide bridges. When I convert my pdb file into a gromacs file, all the
disulfide bridges are still connected (inter- and intra-chain). However,
when I perform a short optimization of the structure (in vacuum), the
inter-chain disulfide bridges are broken because the bond distance is too
large (around 5 and 6 Å). My idea is to use distance restraint to “limit”
the maximum distance between the different sulfure atoms to roughly 2 Å.
However, my problem is that I do not know what residue names I have to use
to differentiate the sulfuret atoms from different chains. Below, you can
find two cysteines (from the itp file) from different chains that I would
like to bind. The question is: If I want to use distance restraint between
these two residues, what is the information that I have to put in the ai
and aj fields of the position restraint table?



     Thank you very much for your help and happy new year for all of you.



     Oscar



                                               CYS in chain A

; residue 897 CYS rtp CYS2 q  0.0

   315        NH1    897    CYS      N    315      -0.47     14.007   ;
qtot 2.53

   316          H    897    CYS     HN    316       0.31      1.008   ;
qtot 2.84

   317        CT1    897    CYS     CA    317       0.07     12.011   ;
qtot 2.91

   318         HB    897    CYS     HA    318       0.09      1.008   ;
qtot 3

   319        CT2    897    CYS     CB    319       -0.1     12.011   ;
qtot 2.9

   320         HA    897    CYS    HB1    320       0.09      1.008   ;
qtot 2.99

   321         HA    897    CYS    HB2    321       0.09      1.008   ;
qtot 3.08

   322         SM    897    CYS     SG    322      -0.08      32.06   ;
qtot 3

   323          C    897    CYS      C    323       0.51     12.011   ;
qtot 3.51

   324          O    897    CYS      O    324      -0.51     15.999   ;
qtot 3



                                               CYS in chain B

; residue 445 CYS rtp CYS  q  0.0

  3451        NH1    445    CYS      N   3451      -0.47     14.007   ;
qtot 5.53

  3452          H    445    CYS     HN   3452       0.31      1.008   ;
qtot 5.84

  3453        CT1    445    CYS     CA   3453       0.07     12.011   ;
qtot 5.91

  3454         HB    445    CYS     HA   3454       0.09      1.008   ;
qtot 6

  3455        CT2    445    CYS     CB   3455      -0.11     12.011   ;
qtot 5.89

  3456         HA    445    CYS    HB1   3456       0.09      1.008   ;
qtot 5.98

  3457         HA    445    CYS    HB2   3457       0.09      1.008   ;
qtot 6.07

  3458          S    445    CYS     SG   3458      -0.23      32.06   ;
qtot 5.84

  3459         HS    445    CYS    HG1   3459       0.16      1.008   ;
qtot 6

  3460          C    445    CYS      C   3460       0.51     12.011   ;
qtot 6.51

  3461          O    445    CYS      O   3461      -0.51     15.999   ;
qtot 6