Hi,
You could also try cpptraj and use the strip command and select by
element to remove all hydrogen atoms, using e.g. the following input:
parm pdbname
trajin pdbname
strip ./H
trajout noH.pdb
-Dan
On Wed, Apr 15, 2015 at 12:35 AM, muhammad tahir ayub
<tahirgp0.gmail.com> wrote:
> Dear All
> While editing the pdb we need to delete the hydrogens, I have
> used the following commands but all the hydrogens were not deleted
>
> reduce -trim pdbnameH > pdbname
>
>
>
> *awk '$1=="ATOM" && substr($3,1,1)!="H"' input.pdb > output.pdb*
>
>
> *what can i do for the deletion of all Hydrogen atoms from the pdb
> filekindly help me in this regard*
>
>
> *Thanks in advance*
> *Muhammad Tahir*
> *Ayub*
>
> *Junior Research Fellow*
>
> *H.E.J Research Institute of Chemistry*
>
> *International Centre for chemical and Biological Sciences*
>
> *University of Karachi, Pakistan*
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Apr 15 2015 - 08:30:11 PDT
