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

majid hasan pu_majidhasan at yahoo.com
Sun Apr 10 00:03:11 CEST 2011

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? 

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?

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