Re: how to generate DNA psf files?

From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Aug 05 2009 - 09:10:25 CDT

An alternative, not necessarily any worse or better (but more work) than
Roman's suggestion, is to strip the hydrogens from your NAMOT generated
structure by:
Load into VMD and open Extensions>Tk console. Make sure DNA is the "top"
molecule. In Tk console type "set sel [atomselect top noh]", then "$sel
writepdb DNA-no-hydrogens.pdb"

This will create a DNA-no-hydrogens.pdb file which can be used during psf
generation with "guesscoords" which will automatically insert the hydrogens
with their correct names. But as Roman suggested, the names are typically
of little consequence.

Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Fri, Jul 31, 2009 at 12:22 AM, Roman Petrenko <rpetrenko_at_gmail.com>wrote:
> 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<yuhuihe_at_ime.pku.edu.cn> 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
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:19 CST