"orderparam" should contain your calculated order parameters.
On page 615 of the new Amber15 manual you can find a description of the
output files:
"The number of defined IRED vectors should match the number of eigenmodes
calculated. Autocorrelation functions for each mode and the corresponding
correlation time tm will be written to filename.cmt. Autocorrelation
functions for each vector will be written to filename.cjt. Relaxation rates
and NOEs for each N-H vector will be written to <filename> or added to the
the end of the standard
output."
-Christina
On Tue, May 5, 2015 at 10:12 AM, Sylvester Tumusiime <stumusii.uno.edu>
wrote:
> Dear Christina,
>
> Thank you for your help. I have now performed the IRED and i get an
> output with the following files:
>
> 1. v0.cmt
> 2. v0.cjt
> 3. orderparam
> 4. ired.vec
> 5. noe
>
> I am guessing that the orderparam is the file that i should contains my
> complete data of interest and that the other files are supoort files with
> the details?
>
> Thanks alot!
>
> S.
>
> ________________________________________
> From: Christina Bergonzo [cbergonzo.gmail.com]
> Sent: Tuesday, May 05, 2015 10:52 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] IRED
>
> Hi,
>
> I think your problem is here:
>
> >matrix ired matired order 2
> >diagmatrix ired vecs 0 out ired.vec name ired.vec
>
> You have an extra space before matired, and you don't assign the matrix to
> a data set called matired using "name."
>
> Try this instead:
> matrix ired name matired order 2
> diagmatrix matired vecs 0 out ired.vec name ired.vec
>
> Or you could try deleting the "matired" part from your original input.
>
> Hope this helps,
> Christina
>
>
> On Tue, May 5, 2015 at 9:40 AM, Sylvester Tumusiime <stumusii.uno.edu>
> wrote:
>
> >
> > Dear Amber users,
> > I have a question concerning the use of IRED to determine order
> > parameters
> > for my alkyl tail (only C-C bonds).
> > I setup a Cpptraj based IRED approach as follows:
> >
> > trajin POP.netcdf 1 100000000 1
> >
> > vector v0 .C13 ired .C14
> >
> > vector v1 .C14 ired .C15
> >
> > vector v2 .C15 ired .C16
> >
> > vector v3 .C16 ired .C17
> >
> > vector v4 .C17 ired .C6
> >
> > vector v5 .C6 ired .C7
> >
> > vector v6 .C7 ired .C8
> >
> > vector v7 .C8 ired .C9
> >
> > vector v8 .C9 ired .C10
> >
> > vector v9 .C10 ired .C11
> >
> > vector v10 .C11 ired .C12
> >
> > matrix ired matired order 2
> >
> > diagmatrix ired vecs 0 out ired.vec name ired.vec
> >
> > ired relax CCdist 1.02 freq 500.0 tstep 0.2 tcorr 100.0 out v0.out
> > noefile
> > noe order 2
> >
> > However, when i try to run the program, i get the following error in
> my
> > output file:
> >
> > CPPTRAJ: Trajectory Analysis. V13.15
> >
> > ___ ___ ___ ___
> >
> > | \/ | \/ | \/ |
> >
> > _|_/\_|_/\_|_/\_|_
> >
> > AmberParm Title: [default_name]
> >
> > Radius Set: modified Bondi radii (mbondi)
> >
> > INPUT: Reading Input from STDIN
> >
> > [trajin POP.netcdf 1 100000000 1]
> >
> > [POP.netcdf] contains 2000 frames.
> >
> > Warning: stop 100000000 > #Frames (2000), setting to max.
> >
> > [vector v0 .C13 ired .C14]
> >
> > VECTOR: Type Mask, IRED, mask [.C13], second mask [.C14]
> >
> > [vector v1 .C14 ired .C15]
> >
> > VECTOR: Type Mask, IRED, mask [.C14], second mask [.C15]
> >
> > [vector v2 .C15 ired .C16]
> >
> > VECTOR: Type Mask, IRED, mask [.C15], second mask [.C16]
> >
> > [vector v3 .C16 ired .C17]
> >
> > VECTOR: Type Mask, IRED, mask [.C16], second mask [.C17]
> >
> > [vector v4 .C17 ired .C6]
> >
> > VECTOR: Type Mask, IRED, mask [.C17], second mask [.C6]
> >
> > [vector v5 .C6 ired .C7]
> >
> > VECTOR: Type Mask, IRED, mask [.C6], second mask [.C7]
> >
> > [vector v6 .C7 ired .C8]
> >
> > VECTOR: Type Mask, IRED, mask [.C7], second mask [.C8]
> >
> > [vector v7 .C8 ired .C9]
> >
> > VECTOR: Type Mask, IRED, mask [.C8], second mask [.C9]
> >
> > [vector v8 .C9 ired .C10]
> >
> > VECTOR: Type Mask, IRED, mask [.C9], second mask [.C10]
> >
> > [vector v9 .C10 ired .C11]
> >
> > VECTOR: Type Mask, IRED, mask [.C10], second mask [.C11]
> >
> > [vector v10 .C11 ired .C12]
> >
> > VECTOR: Type Mask, IRED, mask [.C11], second mask [.C12]
> >
> > [matrix ired matired order 2]
> >
> > MATRIX: Calculating ired matrix, output is by atom
> >
> > 11 IRED vecs, Order of Legendre polynomials: 2
> >
> > Start: 1 Stop: Final frame
> >
> > Warning: [matrix] Not all arguments handled: [ matired ]
> >
> > [diagmatrix matired vecs 0 out ired.vec name ired.vec]
> >
> > I would appreciate any help concerning what i can do to eliminate the
> > error.
> >
> > Thanks,
> >
> > S
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ---------------------------------------------------------------------------------------
> Christina Bergonzo, PhD
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> 30 South 2000 East, Rm. 201
> Salt Lake City, UT 84112-5820
> Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652 / Fax: (801) 585-6208
>
> ---------------------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
---------------------------------------------------------------------------------------
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Received on Tue May 05 2015 - 09:30:03 PDT
