From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Jan 26 2004 - 17:51:12 CST
I suppose you could use the CHARMM 19 topology files, but that would leave
polar hydrogens. As an alternative, you could write a script in VMD to
find all of the hydrogen atoms and then use the psfgen delatom command to
remove them before writing out the psf and pdb files. You shouldn't run a
simulation using these, so I'm not sure what your reason for making a psf
file is (unless VMD is guessing bonds incorrectly).
-Jim
On Fri, 23 Jan 2004, Michael Grabe wrote:
> NAMD list,
>
> I use psfgen to construct my psf file. Is there an easy way to get a
> final structure with no hydrogen atoms? I start from files
> that don't have any hydrogen atoms.
>
> -Michael
> ------------------------------------------------------------------------
> --------------------------
> Michael Grabe, Ph.D.
> Post-doctoral Fellow
> Howard Hughes Medical Institute
> University of California, San Francisco
> 533 Parnassus Ave.
> San Francisco, CA 94143
> mgrabe_at_itsa.ucsf.edu
> tel: ++ 415.476.6585
> http://itsa.ucsf.edu/~mgrabe
>
>
>
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