[gmx-users] error in umbrella sampling tutorial

Ayesha Fatima ayeshafatima.69 at gmail.com
Thu Apr 23 14:47:47 CEST 2015

Dear Justin,
I am learning to use the steered dynamics method implemented in
gromacs. somehow your website is not accessible today so i cannot
download the modified files of the fibrils for simulation. so i
started withe the original file 2BEG.pdb and if i dont select the N
and C termini modifications i get the 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.

Could you guide me through the issue?
Thank you
Ayesha Fatima
PhD candidate, UM, Malaysia

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