Right. Even if you somehow force pdb2gmx to write a topology in this case, the
bonds are not correct and the termini are incomplete. That will hopefully be
resolved when the bug is fixed. For now, you have a workaround. Just use
"-chainsep interactive" and you will get a proper topology.
-Justin
I understand now.
Thank you very much for your help.
Sincerely yours,
Hsin-Lin
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