[gmx-users] Dangling bond error for dna
pu_majidhasan at yahoo.com
Sun Apr 10 19:05:38 CEST 2011
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.
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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
-- gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
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...
More information about the gromacs.org_gmx-users