[gmx-users] pdb2gmx and cyclic molecules

Rebeca García Fandiño regafan at hotmail.com
Mon Nov 7 13:30:35 CET 2016

Dear Gromacs users,

I am trying to simulate a cyclic peptide composed by 8 residues. I have created specbond.dat file to make a new bond between the first (ARG) and the last (TRP) residues from the pdb:


ARG     N       1       TRP     C       1       0.13    ARG  TRP

When I execute pdb2gmx with the options -missing and -ter (selecting manually None), as I have seen in the Gromacs list, I get this error:

pdb2gmx -f cyclic_peptide.pdb -ter -missing -ignh

Back Off! I just backed up topol.top to ./#topol.top.3#
Processing chain 1 (89 atoms, 8 residues)
Identified residue ARG1 as a starting terminus.
Identified residue TRP8 as a ending terminus.
1 out of 1 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    ARG1    ARG2    TRP4    TRP6
                      N1     N12     C44     C66
    ARG2     N12   0.349
    TRP4     C44   0.889   0.783
    TRP6     C66   0.703   0.862   0.631
    TRP8     C88   0.130   0.436   0.892   0.631
Linking ARG-1 N-1 and TRP-8 C-88...
Select start terminus type for ARG-1
 0: NH3+
 1: NH2
 2: None
Start terminus ARG-1: None
Select end terminus type for TRP-8
 0: COO-
 1: COOH
 2: CT2
 3: CT3
 4: None
End terminus TRP-8: None

Program pdb2gmx, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/pdb2top.c, line: 1035

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Could anyone help to solve this, please?

Best wishes,


Santiago de Compostela University

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