HI Dan,
The command I used was:
for i in {1..128};do
cpptraj $top <<EOF
trajin $path/reImaged-bcmLyo25perR.nc 15001 60000 #60000
vector v1 principal z
vector v2 :$i.C52 :$i.C61
vector v3 :$i.C64 :$i.C69
vectormath vec1 v1 vec2 v2 out dataFiles-only/angleZ-chainC12-lipid-$i.dat
name AngleZ-C12 dotangle
vectormath vec1 v1 vec2 v3 out dataFiles-only/angleZ-chainC8-lipid-$i.dat
name AngleZ-C8 dotangle
EOF
done
Previously there was white space after z. That's why it showed [z ] in the
error before. Once the white space fixed, the calculation run fine.
Thanks for your kind help and guide.
Best reagards
Vijay
On Mon, Mar 16, 2015 at 9:58 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> That shouldn't happen since cpptraj removes whitespace from input commands.
> Are you enclosing your input commands in quotes or something?
>
> -Dan
>
> On Monday, March 16, 2015, Vijay Achari <glycoamber.gmail.com> wrote:
>
> > There was a space after "z", as below:
> > [vector v1 principal z ]
> >
> > This should be
> >
> > [vector v1 principal z]
> >
> > Regards
> >
> >
> >
> >
> >
> > On Fri, Mar 13, 2015 at 11:40 AM, Vijay Achari <glycoamber.gmail.com
> > <javascript:;>> wrote:
> >
> > > OK,
> > >
> > > Let me update the cpptraj and test it again.
> > > Vj
> > >
> > > On Fri, Mar 13, 2015 at 11:15 AM, Daniel Roe <daniel.r.roe.gmail.com
> > <javascript:;>>
> > > wrote:
> > >
> > >> On Thu, Mar 12, 2015 at 7:24 PM, Vijay Achari <glycoamber.gmail.com
> > <javascript:;>>
> > >> wrote:
> > >> > [vector v1 principal z ]
> > >> > VECTOR: Type Principal X, mask [*]
> > >> > Error: [vector] Not all arguments handled: [ z ]
> > >>
> > >> That's weird - when I run the same command I get:
> > >>
> > >> > vector v1 principal z
> > >> VECTOR: Type Principal Z, mask [*]
> > >>
> > >> I notice that your CPPTRAJ is a bit out of date. Try updating to the
> > >> latest version (14.25) and see if that helps. Also make sure all of
> > >> your cpptraj test cases are passing.
> > >>
> > >> -Dan
> > >>
> > >> > 1 errors encountered reading input.
> > >> > TIME: Total execution time: 0.0568 seconds.
> > >> >
> > >> > vijay.micelle
> > >>
> >
> :~/Simulation/chapter6-lyo-paper3-Vj/lyo-Analysis2/struc-10-tail-to-Z-angle-distribution/Chain-Angle-distribution-betaLyo25perR$
> > >> >
> > >> >
> > >> > Thank you.
> > >> >
> > >> > On Thu, Mar 12, 2015 at 11:20 PM, Daniel Roe <
> daniel.r.roe.gmail.com
> > <javascript:;>>
> > >> wrote:
> > >> >
> > >> >> Hi,
> > >> >>
> > >> >> On Thu, Mar 12, 2015 at 8:00 AM, Vijay Achari <
> glycoamber.gmail.com
> > <javascript:;>>
> > >> >> wrote:
> > >> >> > *vector v1 principal z vector v2 :1.C50 :1.C80vectormath vec1
> > v1
> > >> >> vec2
> > >> >> > v2 out vectorTimesdat name chainAngle dotangle*
> > >> >> > But I get error.
> > >> >>
> > >> >> Your input is mangled - seems like your newlines are not making it
> to
> > >> >> your email. Make sure you're sending everything in plain text mode.
> > >> >> Also, don't just say you got an "error" - actually report the
> *exact*
> > >> >> error message, otherwise our chances of effectively helping you are
> > >> >> slim.
> > >> >>
> > >> >> -Dan
> > >> >>
> > >> >> --
> > >> >> -------------------------
> > >> >> Daniel R. Roe, PhD
> > >> >> Department of Medicinal Chemistry
> > >> >> University of Utah
> > >> >> 30 South 2000 East, Room 307
> > >> >> Salt Lake City, UT 84112-5820
> > >> >> http://home.chpc.utah.edu/~cheatham/
> > >> >> (801) 587-9652
> > >> >> (801) 585-6208 (Fax)
> > >> >>
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
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> > >> >>
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> > >>
> > >>
> > >>
> > >> --
> > >> -------------------------
> > >> Daniel R. Roe, PhD
> > >> Department of Medicinal Chemistry
> > >> University of Utah
> > >> 30 South 2000 East, Room 307
> > >> Salt Lake City, UT 84112-5820
> > >> http://home.chpc.utah.edu/~cheatham/
> > >> (801) 587-9652
> > >> (801) 585-6208 (Fax)
> > >>
> > >> _______________________________________________
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> > >> http://lists.ambermd.org/mailman/listinfo/amber
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 16 2015 - 11:00:07 PDT
