[gmx-users] Question

Igor Shchechkin shch406 at gmail.com
Sat Jan 10 16:21:25 CET 2015

Dear Gromacs users,

I have obtained the error:
"There is a dangling bond at at least one of the terminal ends...",

running pdb2gmx (4.6.5 version) with the command:

pdb2gmx -f J.pdb -o J.gro -p J.top J.itp.

PDB file 1BJ5 from RCSB was used; 'A' chain and five ligand molecules
attached to it were taken, all heavy atoms restored and OXT atom added
with SwissPDBViewer 4.00 to the C termini:

ATOM   4652  OXT LEU A 585      -9.378  -4.234  37.788  1.00 99.99

To avoid "dangling bond" error I tried both N- and C- terminii special
residues as follows:

ATOM      1  N   NASPA   1      57.277  12.540  12.230  1.00 99.99
ATOM      1  N  NASP A   1      57.277  12.540  12.230  1.00 99.99

This yielded new error instead:
"residue 'HISE' not found in residue topology database"
(But I really haven't such residue name in my PDB!)

I use self-made force field combined from GAFF parameters for ligands,
AMBER99 for protein and tip3p for water,
however I already succesfully perfomed modeling of the same pdb with
the same force field by 4.5.3 version.

Could you, please, help me?

Best regards,
Igor Shchechkin

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