[gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 61

[Nikhil Maroli]

Thanks Mark and Joao
I'm  able to make peptide bond for the Cyclic peptide using specbond.dat
but there is a additional Oxygen and Hydrogen atom on the Carbon and
Nitrogen atom.when i run pdb2gmx selected Amber forcefield  it didnt ask
for the terminals and created topology with amid bond for the cyclic
ring.but when i select the CHARMM forcefield it asking for the terminals
and selected NONE but  it shows the error even after done as you said
before ( Remove the chain ID or make them all chain A. )

*There is a dangling bond at at least one of the terminal ends. Fix
yourcoordinate
file, add a new terminal database entry (.tdb), or select the
 proper existing terminal entry.**For more information and tips for
troubleshooting, please check the GROMACS*

Thanks