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
---------------------------------------------------------------------------------------
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Received on Tue May 05 2015 - 09:30:02 PDT
