Thanks a lot for the corrections.The errors in the rms lines were probably ignored and did not give much error messages, fitting was done using Ca only. I removed that line and the imaging altogether. I modified the ired script by specifing the N and H atom within a residue. It still gives the same error message:
Error: No modes data specified: use 'modes <name>'.
Error: Could not setup analysis [ired]):
It is the last line that give the error, but it is exactly the same as it is in Section 28.15.4. I attached the ired.vec file.
Kris
Script for processing the trajectory:
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
strip :WAT
strip :Cl-
trajout wAnTx_prodNPT-100ns.netcdf netcdf
Here is the output:> cpptraj ../wAnTx_solv_ion.top < add_strip_image_centre_rms.in
CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 08/04/15 18:43:06
| Available memory: 145.191 MB
Reading '../wAnTx_solv_ion.top' as Amber Topology
INPUT: Reading Input from STDIN
[trajin ../wAnTx_prodNPT1.mdcrd]
Reading '../wAnTx_prodNPT1.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT2.mdcrd]
Reading '../wAnTx_prodNPT2.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT3.mdcrd]
Reading '../wAnTx_prodNPT3.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT4.mdcrd]
Reading '../wAnTx_prodNPT4.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT5.mdcrd]
Reading '../wAnTx_prodNPT5.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT6.mdcrd]
Reading '../wAnTx_prodNPT6.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT7.mdcrd]
Reading '../wAnTx_prodNPT7.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT8.mdcrd]
Reading '../wAnTx_prodNPT8.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT9.mdcrd]
Reading '../wAnTx_prodNPT9.mdcrd' as Amber NetCDF
[trajin ../wAnTx_prodNPT10.mdcrd]
Reading '../wAnTx_prodNPT10.mdcrd' as Amber NetCDF
[strip :WAT]
STRIP: Stripping atoms in mask [:WAT]
[strip :Cl-]
STRIP: Stripping atoms in mask [:Cl-]
[trajout wAnTx_prodNPT-100ns.netcdf netcdf]
Writing 'wAnTx_prodNPT-100ns.netcdf' as Amber NetCDF
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'wAnTx_solv_ion.top', 13831 atoms, 4467 res, box: Trunc. Oct., 4433 mol, 4425 solvent, 10000 frames
INPUT TRAJECTORIES:
0: 'wAnTx_prodNPT1.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
1: 'wAnTx_prodNPT2.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
2: 'wAnTx_prodNPT3.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
3: 'wAnTx_prodNPT4.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
4: 'wAnTx_prodNPT5.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
5: 'wAnTx_prodNPT6.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
6: 'wAnTx_prodNPT7.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
7: 'wAnTx_prodNPT8.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
8: 'wAnTx_prodNPT9.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
9: 'wAnTx_prodNPT10.mdcrd' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top (Trunc. Oct. box) (reading 1000 of 1000)
Coordinate processing will occur on 10000 frames.
OUTPUT TRAJECTORIES:
'wAnTx_prodNPT-100ns.netcdf' is a NetCDF AMBER trajectory, Parm wAnTx_solv_ion.top: Writing 10000 frames (1-Last, 1)
TIME: Run Initialization took 0.0001 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'wAnTx_solv_ion.top' (2 actions):
0: [strip :WAT]
Stripping 13275 atoms.
Stripped parm: 'wAnTx_solv_ion.top', 556 atoms, 42 res, box: Trunc. Oct., 8 mol
1: [strip :Cl-]
Stripping 7 atoms.
Stripped parm: 'wAnTx_solv_ion.top', 549 atoms, 35 res, box: Trunc. Oct., 1 mol
----- wAnTx_prodNPT1.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT2.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT3.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT4.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT5.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT6.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT7.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT8.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT9.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- wAnTx_prodNPT10.mdcrd (1-1000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 10000 frames and processed 10000 frames.
TIME: Trajectory processing: 6.6590 s
TIME: Avg. throughput= 1501.7279 frames / second.
ACTION OUTPUT:
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 6.7081 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
Here is the ired script:
> trajin ../wAnTx_prodNPT-100ns.netcdf netcdf
vector v2 :2.N ired :2.H
vector v3 :3.N ired :3.H
vector v4 :4.N ired :4.H
vector v5 :5.N ired :5.H
vector v6 :6.N ired :6.H
vector v8 :8.N ired :8.H
vector v9 :9.N ired :9.H
vector v10 :10.N ired :10.H
vector v11 :11.N ired :11.H
vector v12 :12.N ired :13.H
vector v13 :13.N ired :13.H
vector v14 :14.N ired :14.H
vector v15 :15.N ired :15.H
vector v16 :16.N ired :16.H
vector v17 :17.N ired :17.H
vector v18 :18.N ired :18.H
vector v19 :19.N ired :19.H
vector v20 :20.N ired :20.H
vector v21 :21.N ired :21.H
vector v22 :22.N ired :22.H
vector v23 :23.N ired :23.H
vector v24 :24.N ired :24.H
vector v25 :25.N ired :25.H
vector v26 :26.N ired :26.H
vector v27 :27.N ired :27.H
vector v28 :28.N ired :28.H
vector v29 :29.N ired :39.H
vector v30 :30.N ired :30.H
vector v31 :31.N ired :31.H
vector v32 :32.N ired :32.H
vector v33 :33.N ired :33.H
vector v34 :34.N ired :34.H
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
Here is the output:
> cpptraj ../wAntx.prmtop < ired.cpptraj.in
CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 08/04/15 18:36:14
| Available memory: 175.918 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: Trajectory box type is 'Trunc. Oct.' but topology box type is 'None'.
Warning: Setting topology box information from trajectory.
[vector v2 :2.N ired :2.H]
VECTOR: Type Mask, IRED, mask [:2.N], second mask [:2.H]
[vector v3 :3.N ired :3.H]
VECTOR: Type Mask, IRED, mask [:3.N], second mask [:3.H]
[vector v4 :4.N ired :4.H]
VECTOR: Type Mask, IRED, mask [:4.N], second mask [:4.H]
[vector v5 :5.N ired :5.H]
VECTOR: Type Mask, IRED, mask [:5.N], second mask [:5.H]
[vector v6 :6.N ired :6.H]
VECTOR: Type Mask, IRED, mask [:6.N], second mask [:6.H]
[vector v8 :8.N ired :8.H]
VECTOR: Type Mask, IRED, mask [:8.N], second mask [:8.H]
[vector v9 :9.N ired :9.H]
VECTOR: Type Mask, IRED, mask [:9.N], second mask [:9.H]
[vector v10 :10.N ired :10.H]
VECTOR: Type Mask, IRED, mask [:10.N], second mask [:10.H]
[vector v11 :11.N ired :11.H]
VECTOR: Type Mask, IRED, mask [:11.N], second mask [:11.H]
[vector v12 :12.N ired :13.H]
VECTOR: Type Mask, IRED, mask [:12.N], second mask [:13.H]
[vector v13 :13.N ired :13.H]
VECTOR: Type Mask, IRED, mask [:13.N], second mask [:13.H]
[vector v14 :14.N ired :14.H]
VECTOR: Type Mask, IRED, mask [:14.N], second mask [:14.H]
[vector v15 :15.N ired :15.H]
VECTOR: Type Mask, IRED, mask [:15.N], second mask [:15.H]
[vector v16 :16.N ired :16.H]
VECTOR: Type Mask, IRED, mask [:16.N], second mask [:16.H]
[vector v17 :17.N ired :17.H]
VECTOR: Type Mask, IRED, mask [:17.N], second mask [:17.H]
[vector v18 :18.N ired :18.H]
VECTOR: Type Mask, IRED, mask [:18.N], second mask [:18.H]
[vector v19 :19.N ired :19.H]
VECTOR: Type Mask, IRED, mask [:19.N], second mask [:19.H]
[vector v20 :20.N ired :20.H]
VECTOR: Type Mask, IRED, mask [:20.N], second mask [:20.H]
[vector v21 :21.N ired :21.H]
VECTOR: Type Mask, IRED, mask [:21.N], second mask [:21.H]
[vector v22 :22.N ired :22.H]
VECTOR: Type Mask, IRED, mask [:22.N], second mask [:22.H]
[vector v23 :23.N ired :23.H]
VECTOR: Type Mask, IRED, mask [:23.N], second mask [:23.H]
[vector v24 :24.N ired :24.H]
VECTOR: Type Mask, IRED, mask [:24.N], second mask [:24.H]
[vector v25 :25.N ired :25.H]
VECTOR: Type Mask, IRED, mask [:25.N], second mask [:25.H]
[vector v26 :26.N ired :26.H]
VECTOR: Type Mask, IRED, mask [:26.N], second mask [:26.H]
[vector v27 :27.N ired :27.H]
VECTOR: Type Mask, IRED, mask [:27.N], second mask [:27.H]
[vector v28 :28.N ired :28.H]
VECTOR: Type Mask, IRED, mask [:28.N], second mask [:28.H]
[vector v29 :29.N ired :39.H]
VECTOR: Type Mask, IRED, mask [:29.N], second mask [:39.H]
[vector v30 :30.N ired :30.H]
VECTOR: Type Mask, IRED, mask [:30.N], second mask [:30.H]
[vector v31 :31.N ired :31.H]
VECTOR: Type Mask, IRED, mask [:31.N], second mask [:31.H]
[vector v32 :32.N ired :32.H]
VECTOR: Type Mask, IRED, mask [:32.N], second mask [:32.H]
[vector v33 :33.N ired :33.H]
VECTOR: Type Mask, IRED, mask [:33.N], second mask [:33.H]
[vector v34 :34.N ired :34.H]
VECTOR: Type Mask, IRED, mask [:34.N], second mask [:34.H]
[matrix ired name matired order 2]
MATRIX: Calculating IRED matrix, output is by atom.
32 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: 0.0131 seconds. From: David A Case <david.case.rutgers.edu>
To: Kris Feher <kris.feher.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, August 4, 2015 3:44 PM
Subject: Re: [AMBER] ired analysis: No modes data specified
On Tue, Aug 04, 2015, Kris Feher wrote:
> rms first out wAnTx_prodNPT-100ns.rmsfit @CA, C,N time 0.01
> center :1-20
> image familiar
> strip :WAT
> strip :Cl-
You should have received lots of error messages/warnings from your first
cpptraj run.
First: you cannot have spaces in the atom selection. Use this:
.CA,C,N
The "time" option doesn't make any sense for an rms operation.
After you do an RMS fit, you can no longer image the trajectory. If you have
only a single chain as a macromolecule, there is probably no need to image
the trajectory at all: just strip the waters and ions first, then use that
trajectory for subsequent ired analysis.
I'm not sure if these problems are leading to the further problems you find in
the second cpptraj step, but they should certainly be addressed.
> vector v2 :2 ired :2
This is not correct: you are constructing a vector from to center of mass
of residue 2 *to* the center of mass of residue 2: i.e. a null vector.
See Section 29.14.5 for examples of ired analysis. You generally want to
define (for example) N-H vectors in various residues.
...hope this helps....dac
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Received on Tue Aug 04 2015 - 10:30:02 PDT
