how to get psf files of DNA but not RNA with psfgen?

From: ع (he.yuhui.ime_at_gmail.com)
Date: Thu Sep 17 2009 - 06:25:02 CDT

Dear all,

     I construct a single-strand DNA with random sequence within NAMOT, and
then try to generate PSF file of DNA with following VMD script:

set ssDNA ssDna

mol load pdb ${ssDNA}.pdb

set sel [atomselect top noh]
$sel writepdb DNA-no-hydrogens.pdb

package require psfgen
topology top_all27_na.rtf

segment S {pdb DNA-no-hydrogens.pdb}
coordpdb DNA-no-hydrogens.pdb S
guesscoord
writepdb ${ssDNA}_1.pdb
writepsf ${ssDNA}_1.psf

   However, I find that there are two serious questions:
  1) for the head residue, there is no P atom in original PDB file.
However, there exists P atom on the head residue in the final PDB file.

  2) After checking the final PDB file, I think that the resulting molecule
is Ribose but not Deoxy.

  I guess that not only does the "guesscoord" command add missing H atoms to
the molecule, but it also adds O and P atoms, according to the topology
file.

  What I hope to get is DNA PSF file. I think one approach is to modify
description of residues in the topology file. However, this can not deal
with question 1).

  Can anyone give me some suggestions?

  By the way, I am a researcher with background of Microelectronics. So I am
not familiar with biology. I greatly appreciate some easy-understood
suggestions.

  Thanks and best wishes!

-- 
Yuhui He (ع)
Ph. D
Inst. Microelectronics, Chinese Academy of Sciences,
Beijing 100871, China.

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