normal Adding bond

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11 years 2 months ago #1351 by dark_angel83
Adding bond was created by dark_angel83
Dear MARTINI experts,
I am trying to simulate a protein with a cofactor bound to three cys.
I already parametrized the cofactor but I have to link it to the cysteines and for this reason I am trying to use the -link option.
I need to figure out it works, in particular:
1) atom names are referred to the all atoms or coarse grained PDB?
2) the residue index starts from 0,1 or it is the same index of the PDB

Moreover I would like to know whether -link option is supposed to work with other options (i.e. -merge)

Francesco

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11 years 2 months ago #1353 by djurre
Replied by djurre on topic Adding bond
I'm afraid this might not work because the cofactor parameters are not in martinize.py script. You could add them, but it might be easier to add the cofactor by hand.

In case you want to try: The atomnames are CG atoms names, the residue index is the same as in the PDB and I think the link option should work with merge.

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