[gmx-users] monomer's conectivity

[Mark Abraham]

Andrea Muntean wrote:
> I have a *pdb file for a polymer box which I want to use. I defined the 
> residues (the first, the last and the inner monomers).
> Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M 
> monomers each.
> My problem now is how to connect the monomers. What is the best way to 
> do so?

We can't tell yet. You might have a PDB file with each residue in its 
own chain. You might have defined residue topologies without suitable 
connectors. You might be observing a visualization artefact. You might 
have some warnings from pdb2gmx you haven't observed yet.

Mark