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

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 10 00:05:48 CEST 2011

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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