On Wed, Feb 24, 2016, Madhura De wrote:
>
> I use Amber14 suite. I am about to do an NMR refinement of a DNA duplex and
> will be using IRMA (http://www.nmr.chem.uu.nl/Software/irma.php). The input
> file for IRMA requires only protons to be extracted from all-atom
> coordinate or trajectory file.
> Can you tell me the command by which I can extract only the protons from
> mdcrd or pdb file?
If you plan to do much work in this area, learning simple tools like awk or
perl will be very valuable to you. A script like the following should work:
awk 'substr($3,1,1)=="H"' inputpdb-file > outputpdb-file
But cpptraj can also do this:
parm prmtop-file
trajin pdbfile or mdcrdfile
strip '!.H='
trajout outputpdb-file or outputmdcrd-file
go
...dac
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Received on Wed Feb 24 2016 - 05:00:04 PST
