this works for me:
####################################
infiles2=""
infiles2="$infiles2\ntrajin dehydrated2a_${dirNo}.crd "
infiles2="$infiles2\nstrip :WAT "
infiles2="$infiles2\ntrajout dehydrated3_${dirNo}.crd "
echo -ne $infiles2 | ptraj dehydrated2a_${dirNo}.parm
####################################
best regards,
ET
On 28 February 2012 18:03, Ismail, Mohd F. <farid.ou.edu> wrote:
> Thank you all for the quick replies, Dr. Roitberg, Dr. Cheatham.
>
> (also thanks to Jason, Dr. Dupradeau for all the previous replies)
>
> *******************************
> Mohd Farid Ismail
> Graduate Student
> Dept. of Chemistry/Biochemistry
> University of Oklahoma
> Norman 73019
>
> ________________________________________
> From: Thomas Cheatham III [tec3.utah.edu]
> Sent: Tuesday, February 28, 2012 11:54 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Embed Shell Scripting in ptraj script
>
> > I've done a quick search, but couldn't find anything. Is there a way to
> include shell scripting in ptraj script?
>
> No.
>
> > 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
>
> We will consider adding some type of functionality to do this and/or
> wildcards, etc. as I have had issues myself with very large ptraj scripts.
> What I do know to get around this is have csh or Perl scripts that create
> the ptraj script for me (and run ptraj).
>
> --tec3
>
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>
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Received on Wed Feb 29 2012 - 05:00:02 PST
