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
Received on Tue May 05 2015 - 09:00:02 PDT
