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? Thanks, Majid
ssdna.pdb
Description: Binary data
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