[gmx-users] Question

[Justin Lemkul]

On 1/10/15 10:21 AM, Igor Shchechkin wrote:
> 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
> or
> 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?
>

You need to provide the full screen output, including all of your selections. 
There are numerous relevant choices and messages that you haven't included here.

FWIW, if you have a topology from 4.5.3 that worked, it will also work in 4.6.5 
without having to regenerate it.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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