On Sun, Apr 27, 2014 at 8:00 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Hii;
>
> So as per cpptraj script if I use this script I will get a stripped topoly
> which corresponds to stripped .mdcrd
>
> trajin md2.mdcrd
> autoimage
> strip :WAT,Na+ outprefix stripped
> trajout md2_dry.mdcrd
>
> Is ther any quick ptraj or cpptraj script which will generate a
> corresponding pdb as well as topoloy which will correspond to the same
> stripped co-ordinate?
>
> Also say for example because of internet connection issue sometimes taking
> snapshots by transferring coordinate becomes a problem. Any script which
> will help in taking snapshot at a particular time. Say for example I ran a
> 50 ns MD and I want a corresponding PDB which denotes at the point of 30 ns
> any script for that.
>
In addition to Dave's comments, you can add a single line to do this:
trajin md2.mdcrd
autoimage
strip :WAT,Na+ outprefix stripped
outtraj snapshot.pdb onlyframes 30000
trajout md2_dry.mdcrd
Notice the "outtraj" command. This will dump a PDB file from just the
30,000th frame of your trajectory. This would be correct if you wrote a
snapshot every 1 ps and you read all 50 ns of simulation into the same
cpptraj session. Adjust it accordingly to what you are trying to do.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Apr 27 2014 - 07:00:02 PDT
