From: ºÎع»Ô (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 (ºÎع»Ô) Ph. D Inst. Microelectronics, Chinese Academy of Sciences, Beijing 100871, China.
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