EVEN I HAD DONE THAT REDUCE BUT ALSO IT WAS GENERATING THE SAME
ERROR.........
On Tue, Feb 15, 2011 at 7:52 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Another alternative for eliminating hydrogen atoms is to use "reduce",
> which
> is compiled with amber. Typically reduce is used to ADD hydrogens, but it
> can also be used to remove them:
>
> reduce -Trim my.pdb > my_no_h.pdb
>
> Good luck,
> Jason
>
> On Tue, Feb 15, 2011 at 8:36 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > how can we delete that hydrogen atoms
> >
> > If you have no H's in residue names:
> >
> > $ egrep -v H my.pdb > my_no_h.pdb
> >
> > Otherwise look at e.g. awk or perl to select out based on the
> > atom name field.
> >
> > Bill
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 15 2011 - 18:30:02 PST
