[gmx-users] .n2t file for ssDNA

majid hasan pu_majidhasan at yahoo.com
Sat Apr 9 03:58:42 CEST 2011

Oh, yes, I could open it in text editor. I didn't realize that. 


From: Justin A. Lemkul <jalemkul at vt.edu>
To: Gromacs Users' List <gmx-users at gromacs.org>
Sent: Fri, April 8, 2011 6:48:13 PM
Subject: Re: [gmx-users] .n2t file for ssDNA

majid hasan wrote:
> I looked at the error in more detail (output attached), and it says that: 
>Warning: Residue T6 in chain has different type (Other) from starting residue A1 
>(RNA). I had a dna.pdb file so first but its reading the first residue as RNA.
> So to me, problem seems to be that residues are named differently in my dna.pdb 
>file and dna.rtp file of force field. I looked at dna.pdb file using more 
>dna.pdb (output attached), and the residues are named as A, C, G, T, while in 
>Amber's dna.rtp file (attached) these are named as DA3, DC3. Could this be a 
>problem?  If this is, then how do I change the names of residues in .pdb file, 
>which I created it using a different software (3DNA, and Gabedit)?

The names of the residues must conform to the names found in the force field 
.rtp file.  The changes can be made with a text editor, but be careful not to 
shift the spacing of the .pdb file; its format must remain fixed.


> Thanks,
> Majid
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