[gmx-users] struggles with cyclic peptides

Justin Lemkul jalemkul at vt.edu
Sun Sep 13 19:56:01 CEST 2015

On 9/13/15 1:45 PM, Nikhil wrote:
> Thank you very much Justine,
> now it making bond between first and last residue of amino acids but there
> as an extra oxygen atom is coming  when i select any option other than
> None.but when i select None for the second terminals it shows an error
> as
> There is a dangling bond at at least one of the terminal ends. Fix
> yourcoordinate 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*
> should i edit the .tdb file ?

Using "None" as the termini is correct.  You may have to add -missing to the 
command, though this will also cause no H atoms to be built, so your input file 
needs to have them.  Check any topology using -missing very carefully before 
diving into any real simulations.



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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