Topology issues

[fercofas]

I've been able to get the files expected in step 3.2 with the basic usage instructions. Nonetheless, while implementing system minimization, I discovered the issue depicted in the enclosed image.

Is it necessary to take any additional steps in order to carry out the simulation?

Additional information: The in-house Python script generates an itp file that contains the information on both molecules_BB-part-def_VirtGoSites and molecules_0_go-table_VirtGoSites itp files, as well as another itp file that is similar to molecule_0.itp.

[sebtha]

Did you modify the Martini 3 itp file as described in the basic protein tutorial, section B2?

In addition, you should define the variable GO_VIRT at the beginning of the topology file:
#define GO_VIRT
such that the modifications are active and the virtual beads are defined by gmx grompp.

[fercofas]

Yeah, It worked. Thank you very much. I added the corresponding lines to Martitin 3 itp. The variable GO_VIRT was already in the topology file. I suggest this info should be included here because this phrase in the tutorial "Because the main Martini force field .itp should not be changed" is a bit misleading. I'll be testing the protocol with structures with more than one chain.