[gmx-users] Dangling bond error for dna

majid hasan pu_majidhasan at yahoo.com
Sun Apr 10 05:47:40 CEST 2011

.pdb file size was big, so message didn't deliver. Now I have removed atoms from 
pdb file to reduce the size, and the files are attached. 


From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sat, April 9, 2011 7:18:30 PM
Subject: Re: [gmx-users] Dangling bond error for dna

majid hasan wrote:
> Dear All,
> I created .pdb file for dna using gabedit. But when I try to create the 
>topology file I get this error: Fatal error:
> There is a dangling bond at at least one of the terminal ends and the force 
>field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb 
> Output of pdb2gmx, and my input pdb files are attached. Could anyone please 
>suggest why this is happening?

Nothing is attached.


> Thanks,
> Majid

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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