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
>
> _______________________________________________
> AMBER mailing list
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 15 2011 - 18:00:07 PST
