[gmx-users] Dangling bond error for dna

[Justin A. Lemkul]

majid hasan wrote:
> 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.
> 

Perhaps xleap (part of AmberTools), but if your input has a bunch of incorrect 
atoms, I don't know how well it deals with replacing them.  I seem to remember 
that it just writes new atoms and doesn't necessarily clean up the old ones, but 
my memory could be incorrect or the program may have been improved since last I 
tried it.

http://ambermd.org/#AmberTools

-Justin

> 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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> -- gmx-users mailing list    gmx-users at gromacs.org 
> <mailto: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 
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

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

========================================