[gmx-users] Dangling bond error for dna

[majid hasan]

Is there any software that generates .pdb file consistent with amber forcefield 
requirements? I tried 3DNA, and GABEDIT, but 3DNA doesn't name residues in 
correct format i.e DX, and gabedit names every residue as DX3.

Thanks,
Majid



________________________________
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

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search 
before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or 
send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110410/7732d154/attachment.html>