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?
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