[gmx-users] error in umbrella sampling tutorial

Justin Lemkul jalemkul at vt.edu
Thu Apr 23 23:36:15 CEST 2015

On 4/23/15 8:47 AM, Ayesha Fatima wrote:
> Dear Justin,
> I am learning to use the steered dynamics method implemented in
> gromacs. somehow your website is not accessible today so i cannot

Server has been accessible all day; no idea why it wouldn't be working.

> 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?

You can't sensibly choose "none" for terminal patching if there are no capping 
groups.  My coordinates have an acetyl cap on the N-terminus of each peptide, 
which is why this works.



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


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