[gmx-users] Dangling bond error for dna

majid hasan pu_majidhasan at yahoo.com
Sun Apr 10 18:58:33 CEST 2011

Okay, thank you. I'll try to fix it.


From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Sun, April 10, 2011 4:17:59 AM
Subject: Re: [gmx-users] Dangling bond error for dna

majid hasan wrote:
> Sorry, the pdb file is bigger than 50k so it won't attach, so its pasted below. 
>Output of pdb2gmx is attached.

You have numerous problems with this .pdb file:

1. All residues are listed as being the 3' end form.  Your chain should start 
with a 5' end, include the "middle" residues, and end with a 3' form.

2. 5' ends do not have phosphate on them, per force field convention.

3. You have various incorrect atoms, and some incorrect atom names.

Please refer to the dna.rtp file for your chosen force field to understand its 
expectations.  Then you will need to manually fix your .pdb file by renaming, 
replacing, or removing whatever is in conflict.


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

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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