[gmx-users] pdb2gmx -ter with cyclic peptide

andrea spitaleri spitaleri.andrea at hsr.it
Thu Jan 19 15:24:44 CET 2012

Hi there,
normally to generate a cyclic peptide I use to edit specbond.dat to force the bond between the N- 
and C-termini and I use the -ter flag into pdb2gmx tool in order to avoid to add hydrogens and 
oxygen to the end of the peptide. This was okay until the gromacs version 4.0.5 with opls ff.

Now using gromacs 4.5.3 with opls ff I get this message:

"There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry."

did something change or is is a bug? I have checked in the mailing list and I did not find any answer.

thanks in advance for any help


Andrea Spitaleri PhD
Dulbecco Telethon Institute c/o Raffaele Scientific Institute
Biomolecular NMR Laboratory Dibit2 Basilica 3A2
Via Olgettina 58
20132 Milano
Tel: 0039-0226434348
Fax: 0039-0226434153

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