[gmx-users] Dangling bond error, -ter does not fix
THOMAS.LIPSCOMB at PURCHASE.EDU
Wed Oct 29 22:05:41 CET 2014
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.
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.
/usr/local/gromacs/bin/gmx pdb2gmx -f model1.pdb -o model1_processed.gro -ignh -ter -water spc
Program gmx, VERSION 5.0.1
Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091
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?
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