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
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