You could use Tk console in VMD and then in order to remove H from pdb do:
mol load pdb your.pdb
set sel [atomselect top "not hydrogen"]
$sel writepdb new_noH.pdb
Regards,
Sofia
> On Wed, 15 Apr 2015 11:35:51 +0500
> muhammad tahir ayub <tahirgp0.gmail.com> wrote:
>
>
>> reduce -trim pdbnameH > pdbname
>>
>> *awk '$1=="ATOM" && substr($3,1,1)!="H"' input.pdb > output.pdb*
>
> While it is generally a bad idea to use awk on a fixed-column format
> like PDB it is unclear to me why either command would not strip all
> hydrogens. Ok, the awk command would obviously fail if you have
> "HETATM" records. What hydrogens to you still see in the output file?
>
> Cheers,
> Hannes.
>
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Received on Wed Apr 15 2015 - 06:00:07 PDT
