no, there is not, but..
you could write something like this (I am reusing your OWN writing, but
it is not correct)
echo "trajin mytrajectory" >> ptraj.trajin
for ( i=1, i<6, i++)
echo "radial myoutputfile_i 0.1 10 .oxy1,.oxy2,.oxy3 .10i" >> ptraj.trajin
end
ptraj prmtop < ptraj.trajin
Basically, create a script that itself creates a ptraj input file, and
then run that one.
Adrian
On 2/28/12 12:48 PM, Ismail, Mohd F. wrote:
> I've done a quick search, but couldn't find anything. Is there a way to include shell scripting in ptraj script?
>
> For example, lets say I want the radial distribution of all oxygen atoms around 5 ions, so far I have been doing:
>
> trajin mytrajectory
> radial myoutputfile1 0.1 10 .oxy1,.oxy2,.oxy3 .101
> radial myoutputfile2 0.1 10 .oxy1,.oxy2,.oxy3 .102
> radial myoutputfile3 0.1 10 .oxy1,.oxy2,.oxy3 .103
> radial myoutputfile4 0.1 10 .oxy1,.oxy2,.oxy3 .104
> radial myoutputfile5 0.1 10 .oxy1,.oxy2,.oxy3 .105
>
> Is there a way to include scripting like
>
> trajin mytrajectory
> for ( i=1, i<6, i++)
> radial myoutputfile_i 0.1 10 .oxy1,.oxy2,.oxy3 .10i
>
>
>
> *******************************
> Mohd Farid Ismail
> Graduate Student
> Dept. of Chemistry/Biochemistry
> University of Oklahoma
> Norman 73019
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> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Feb 28 2012 - 10:00:04 PST
