Dear All,
I am trying to calculate NMR relaxation parameters from a trajectory using the ired analysis. First I collected the trajectory from 10ns parts into a 100ns .netcdf file without ions and water:
trajin ../wAnTx_prodNPT1.mdcrd
trajin ../wAnTx_prodNPT2.mdcrd
trajin ../wAnTx_prodNPT3.mdcrd
trajin ../wAnTx_prodNPT4.mdcrd
trajin ../wAnTx_prodNPT5.mdcrd
trajin ../wAnTx_prodNPT6.mdcrd
trajin ../wAnTx_prodNPT7.mdcrd
trajin ../wAnTx_prodNPT8.mdcrd
trajin ../wAnTx_prodNPT9.mdcrd
trajin ../wAnTx_prodNPT10.mdcrd
trajout wAnTx_prodNPT-100ns.netcdf netcdf
rms first out wAnTx_prodNPT-100ns.rmsfit @CA, C,N time 0.01
center :1-20
image familiar
strip :WAT
strip :Cl-
Then I used the following script on the 100ns trajectory for the ired analysis as contructed according to the manual:
trajin ../wAnTx_prodNPT-100ns.netcdf netcdf
vector v2 :2 ired :2
vector v3 :3 ired :3
vector v4 :4 ired :4
vector v5 :5 ired :5
vector v6 :6 ired :6
vector v8 :8 ired :8
vector v9 :9 ired :9
vector v10 :10 ired :10
vector v11 :11 ired :11
vector v12 :12 ired :12
vector v13 :13 ired :13
vector v14 :14 ired :14
vector v15 :15 ired :15
vector v16 :16 ired :16
vector v17 :17 ired :17
vector v18 :18 ired :18
vector v19 :19 ired :19
vector v20 :20 ired :20
vector v21 :11 ired :21
vector v22 :12 ired :22
vector v23 :13 ired :23
vector v24 :14 ired :24
vector v25 :15 ired :25
vector v26 :16 ired :26
vector v27 :17 ired :27
vector v28 :18 ired :28
vector v29 :19 ired :29
vector v30 :20 ired :30
vector v31 :11 ired :31
vector v32 :12 ired :32
vector v33 :13 ired :33
vector v34 :14 ired :34
vector v35 :15 ired :35
matrix ired name matired order 2
diagmatrix matired vecs 6 out ired.vec name ired.vec
ired relax NHdist 1.02 freq 500.0 tstep 1.0 tcorr 100.0 out v0.out noefile noe order 2
as the output I got the following message:
> cpptraj ../wAntx.prmtop < ired.cpptraj
CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 08/03/15 21:28:20
| Available memory: 1666.86 MB
Reading '../wAntx.prmtop' as Amber Topology
INPUT: Reading Input from STDIN
[trajin ../wAnTx_prodNPT-100ns.netcdf netcdf]
Reading '../wAnTx_prodNPT-100ns.netcdf' as Amber NetCDF
Warning: NetCDF file time variable defined but empty. Disabling.
Warning: Trajectory box type is 'Trunc. Oct.' but topology box type is 'None'.
Warning: Setting topology box information from trajectory.
[vector v2 :2 ired :2]
VECTOR: Type Mask, IRED, mask [:2], second mask [:2]
[vector v3 :3 ired :3]
VECTOR: Type Mask, IRED, mask [:3], second mask [:3]
[vector v4 :4 ired :4]
VECTOR: Type Mask, IRED, mask [:4], second mask [:4]
[vector v5 :5 ired :5]
VECTOR: Type Mask, IRED, mask [:5], second mask [:5]
[vector v6 :6 ired :6]
VECTOR: Type Mask, IRED, mask [:6], second mask [:6]
[vector v8 :8 ired :8]
VECTOR: Type Mask, IRED, mask [:8], second mask [:8]
[vector v9 :9 ired :9]
VECTOR: Type Mask, IRED, mask [:9], second mask [:9]
[vector v10 :10 ired :10]
VECTOR: Type Mask, IRED, mask [:10], second mask [:10]
[vector v11 :11 ired :11]
VECTOR: Type Mask, IRED, mask [:11], second mask [:11]
[vector v12 :12 ired :12]
VECTOR: Type Mask, IRED, mask [:12], second mask [:12]
[vector v13 :13 ired :13]
VECTOR: Type Mask, IRED, mask [:13], second mask [:13]
[vector v14 :14 ired :14]
VECTOR: Type Mask, IRED, mask [:14], second mask [:14]
[vector v15 :15 ired :15]
VECTOR: Type Mask, IRED, mask [:15], second mask [:15]
[vector v16 :16 ired :16]
VECTOR: Type Mask, IRED, mask [:16], second mask [:16]
[vector v17 :17 ired :17]
VECTOR: Type Mask, IRED, mask [:17], second mask [:17]
[vector v18 :18 ired :18]
VECTOR: Type Mask, IRED, mask [:18], second mask [:18]
[vector v19 :19 ired :19]
VECTOR: Type Mask, IRED, mask [:19], second mask [:19]
[vector v20 :20 ired :20]
VECTOR: Type Mask, IRED, mask [:20], second mask [:20]
[vector v21 :11 ired :21]
VECTOR: Type Mask, IRED, mask [:11], second mask [:21]
[vector v22 :12 ired :22]
VECTOR: Type Mask, IRED, mask [:12], second mask [:22]
[vector v23 :13 ired :23]
VECTOR: Type Mask, IRED, mask [:13], second mask [:23]
[vector v24 :14 ired :24]
VECTOR: Type Mask, IRED, mask [:14], second mask [:24]
[vector v25 :15 ired :25]
VECTOR: Type Mask, IRED, mask [:15], second mask [:25]
[vector v26 :16 ired :26]
VECTOR: Type Mask, IRED, mask [:16], second mask [:26]
[vector v27 :17 ired :27]
VECTOR: Type Mask, IRED, mask [:17], second mask [:27]
[vector v28 :18 ired :28]
VECTOR: Type Mask, IRED, mask [:18], second mask [:28]
[vector v29 :19 ired :29]
VECTOR: Type Mask, IRED, mask [:19], second mask [:29]
[vector v30 :20 ired :30]
VECTOR: Type Mask, IRED, mask [:20], second mask [:30]
[vector v31 :11 ired :31]
VECTOR: Type Mask, IRED, mask [:11], second mask [:31]
[vector v32 :12 ired :32]
VECTOR: Type Mask, IRED, mask [:12], second mask [:32]
[vector v33 :13 ired :33]
VECTOR: Type Mask, IRED, mask [:13], second mask [:33]
[vector v34 :14 ired :34]
VECTOR: Type Mask, IRED, mask [:14], second mask [:34]
[vector v35 :15 ired :35]
VECTOR: Type Mask, IRED, mask [:15], second mask [:35]
[matrix ired name matired order 2]
MATRIX: Calculating IRED matrix, output is by atom.
33 IRED vecs, Order of Legendre polynomials: 2
Matrix data set is 'matired'
Start: 1 Stop: Final frame
[diagmatrix matired vecs 6 out ired.vec name ired.vec]
Changed DataFile 'ired.vec' type to Evecs file for set ired.vec
DIAGMATRIX: Diagonalizing matrix matired and writing modes to ired.vec
Calculating 6 eigenvectors
Storing modes with name: ired.vec
[ired relax NHdist 1.02 freq 500.0 tstep 1.0 tcorr 100.0 out v0.out noefile noe order 2]
Error: No modes data specified: use 'modes <name>'.
Error: Could not setup analysis [ired]
1 errors encountered reading input.
TIME: Total execution time: 0.0296 seconds.
If I execute the without the last ired analysis command I get ired.vec file.I am using freshly installed amber 14 with AmberTools15.
Please, let me know what I can do to find the problem.All the best,Kris
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Received on Tue Aug 04 2015 - 05:30:03 PDT
