An alternative is to use the "reduce" program, which can be used to trim
hydrogen atoms as well as add them.
So it would be something like this:
reduce -Trim your_file.pdb > your_file_nohydrogen.pdb
HTH,
Jason
On Tue, Feb 21, 2012 at 8:27 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Feb 21, 2012, Atila Petrosian wrote:
> >
> > Is there any command in amber to delete all hydrogen atoms of pdb file?
>
> Try this:
>
> awk '$1=="ATOM" && substr($3,1,1)!="H"' input.pdb > output.pdb
>
> (Assumes all hydrogen atom names begin with "H".) Modify as needed.
>
> ...good luck...dac
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 21 2012 - 20:30:02 PST
