[gmx-users] Dangling bond error for dna
pu_majidhasan at yahoo.com
Sun Apr 10 21:54:02 CEST 2011
Okay, I am trying AmberTools as well. Thanks Justin!
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
> *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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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