how to generate DNA psf files?

From: He Yuhui (
Date: Wed Jul 29 2009 - 21:04:27 CDT

Dear All,

   Right now, I have generated pdb files of single-strand DNA with
NAMOT. However, I have no idea how to generate the corresponding psf
files. I have tried following commands within VMD:

set ssDNA atcgatcgatcgatcg

package require psfgen
topology top_all27_na.rtf

segment S {pdb ${ssDNA}.pdb}
coordpdb ${ssDNA}.pdb S
writepdb ${ssDNA}.pdb
writepsf ${ssDNA}.psf

    It does not work.
    First, it is unnecessary to generate so-called missing H atoms,
since all H atoms have been written into pdb files by NAMOT.

    Second, by comparing CHARMM topology files (top_all27_na.rtf) and
pdb files (generated by NAMOT), I find that their naming rules of atoms
should be different. Does it means that when generating psf files in
VMD, the psfgen package could not recognize atoms in pdb files

    Can anyone help me with this DNA psf file generation? Any
suggestions are appreciated!

    Thanks and regards!

Yuhui He

Dr. Yuhui He (何毓辉)
Institute of Microelectronics, Chinese Academy of Sciences
Beijing China, 100029

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