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?
http://www.wwpdb.org/documentation/format32/sect9.html
-Justin
Thanks,
Majid
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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