[gmx-users] Dangling bond error, -ter does not fix

Justin Lemkul jalemkul at vt.edu
Thu Oct 30 02:09:07 CET 2014

On 10/29/14 4:59 PM, LIPSCOMB, THOMAS wrote:
> Dear gmx-users,
> I am following this tutorial to insert one antimicrobial peptide (model1.pdb, attached) into a membrane.  With the goal of inserting several of them to investigate their tertiary structure.

The list does not accept attachments.  Please upload the file to a file-sharing 
service and provide the URL.

> https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial
> However I think that something is wrong with my .tdb files based on the "dangling bond" error below.  Where can I learn (the manual?) about .tdb files (I know nothing about them) or download one that works?  Unfortunately http://www.gromacs.org/Documentation/Errors does not help because the dangling bond error is not there.  I thought that -ter would fix this error but it did not.

It is highly unlikely that there is any need to modify the .tdb file.  The 
contents of these files are described in manual section 5.6.5.

> cd /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP
> /usr/local/gromacs/bin/gmx  pdb2gmx -f model1.pdb -o model1_processed.gro -ignh -ter -water spc
> 13
> 2
> 2

Without knowing which force field you're choosing, I don't know what these 
selections correspond to.  What are you choosing for the termini?

> Program gmx, VERSION 5.0.1
> Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors?

The "dangling bond" error indicates an incomplete terminus, either due to 
missing atoms or incorrect selection of terminus type.



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


More information about the gromacs.org_gmx-users mailing list