[gmx-users] pdb2gmx and cyclic molecules

Nikhil Maroli scinikhil at gmail.com
Fri Nov 11 06:52:45 CET 2016

HI, Rebeca.

The dangling bonds are due to inappropriate selection of terminals.

You need to make lots of changes in respective files to get a gro for
cyclic peptide.If your using charmm ff better try with the server.

Nikhil Maroli

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