[gmx-users] Naming of DNA residues, and structure of .pdb file

majid hasan pu_majidhasan at yahoo.com
Sun Apr 10 00:15:18 CEST 2011

Okay, thanks a lot.


From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sat, April 9, 2011 3:05:48 PM
Subject: Re: [gmx-users] Naming of DNA residues, and structure of .pdb file

majid hasan wrote:
> Dear All,
> I am trying to make sure that the names of dna residues in my .pdb file match 
>with .rtp file in the Amber forcefield. I looked up the residuetypes.dat file 
>(attached), and it gives the names for DNA residues, which are of the form, DX, 
>DX3, DX5, DXN (X=A,C,T,G). So if I have a residue X, then what is the difference 
>between DX, DX3, so on i.e when do I name residue X as DX, and when as DX3, and 
>so on?

DX = normal residue
DX5 = 5' end
DX3 = 3' end

> Moreover, can anyone explain me the format of pdb file (attached) i.e what do 
>different columns represent, so I can change the names of residues without 
>making any error?



> Thanks,
> Majid

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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