Dear gromacs user, I noted a strange behavior in topology generation workflow.
I have a protein whose active site contains a Ni atom linked to 4 Cys. I inserted the 4 bonds by specbonds.dat. When I run pdb2gmx, I have inspected the Linking messages and they fit with the expected topology, I mean pdb2gmx correctly detects the four bonds nickel-sulphur. So I run grompp and the topol.tpr has been correctly generated. Then I compared topol.top and topol.tpr bonds and I noticed that in topol.top there a lot of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium. I dumped topol.tpr through gmxdump, and I noticed that these bonds are no more present and only "right" bonds are present. So, I am wondering why the fake bonds are inserted in topol.top and how grompp detectes these bonds. Francesco
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