GROMACS version: 2020.5
GROMACS modification: No
Dear users,
I find that although I used “gmx pdb2gmx -ss yes” and got the hint like “Link CYS-xxx SG-xxxx and CYS-xxx SG-xxxx(y/n) ?y” my gro file and itp/top file are still almost the same as these files generated without the -ss yes flag.
In addition, when I used chimerax to open gro files (generated with and without -ss yes flag) the disulfide bonds both showed up in these two cases (with and without -ss yes flag).
Thanks!
The .gro file contains only the atom positions (and box vectors, and sometime velocities) but no information about bonds or topology (you can open the file in a text editor to see the format - it is a list of atom with coordinates). The bonds are specified in the topology .top file.
When loading such file in visualization software, the bond are inferred by the software itself using an heuristic: it will decide that two cysteine S close enough together are bonded, and will show them such. Similarly for all other bonds. What is displayed had no relation with the topology which describe the bond - though is is often very close.
If the topology file are exactly identical, that might be a problem. But you say they are “almost identical”. The difference between a cysteine bridge, and none, would be a single bond, which would be a single line in the topology file. By using a diff tool (diff fileA fileB, or a GUI tool like Meld), you can check whether that additional bond has been added in the [ bonds ] section of the topology.
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@ ebriand Thank you for your kind reply.
Actually I did use diff command and found two pdb2gmx generated itp files (-ss yes and -ss not defined) are same (only comment difference).
Furthermore, I can find disulfide bonds parameters in [ bonds ] and [ angles ] in both itp files (-ss yes and -ss not defined).
By the way, I previously thought the cys name might be changed in gro file if disulfide bond formed.
In sum, it seems pdb2gmx may automatically add disulfide bonds even if -ss is not defined (-ss default is no)
That is to be expected. The -ss option, like those that alter protonation state, simply allow the user to override (or explicitly agree with) the default behavior of pdb2gmx, in this case for assigning disulfides based on interatomic distance.
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Thanks for your explanation!