Re: how to generate DNA psf files?

From: Roman Petrenko (
Date: Fri Jul 31 2009 - 00:22:31 CDT

Dear Yuhui,
atom naming is specific to each program, just don't worry and ignore
this if psfgen exits without errors (note some warning will be there,
which can also be ignored).

As you hydgorens, i guess if you remove command guesscoord they will
not be generated.

On Wed, Jul 29, 2009 at 10:04 PM, He Yuhui<> wrote:
> 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
> guesscoord
> 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
> correctly?
>    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

Roman Petrenko
Physics Department
University of Cincinnati

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