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

[LIPSCOMB, THOMAS]

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.

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.




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

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?



Thank you.


Sincerely,

Thomas