[gmx-users] Dangling bond error for dna

[majid hasan]

Okay, I am trying AmberTools as well. Thanks Justin!

Majid



________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Sun, April 10, 2011 10:16:57 AM
Subject: Re: [gmx-users] Dangling bond error for dna



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
> 
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-- ========================================

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

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