On Thu, Apr 16, 2015 at 1:16 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> But since this is a properly formatted PDB file and thus has the element names in columns 77-78 properly designed software should be able to handle this...
FYI cpptraj should be able to handle removing hydrogens from this PDB
(using the input posted previously) since it does make use of the
element column if one is present.
-Dan
>
> BTW, I have noticed that some of the records in your PDB are partially shifted to the left. You have to make sure to properly align those entries as it is likely that software can't handle this. The PDB format is a fixed column format.
>
> ________________________________________
> From: muhammad tahir ayub [tahirgp0.gmail.com]
> Sent: 16 April 2015 19:09
> To: Loeffler, Hannes (STFC,DL,SC)
> Subject: deletion of H atoms for pdb file
>
> Dear Cheers,
> I have attached the following original and edited pdb file i have obtained after applying the
>
> awk '$1=="ATOM" && substr($3,1,1)!="H"' input.pdb > output.pdb
>
> the reduce command just deleted all the data of pdb file
>
> 1cgh.pdb = original pdb file
> 1cgh_ed.pdb = pdb file after application of awk command
>
> Muhammad Tahir Ayub
> Junior Research Fellow
> H.E.J Research Institute of Chemistry
>
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--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
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Received on Thu Apr 16 2015 - 13:00:02 PDT
