Hi,
I have used many times successfully this cpptraj script:
trajin pczn_wt_Final.mdcrd 200 10000000 1
# Average the trajectory.
rms first :1-330.CA
average Avg.rst7 restart
createcrd crd1
run
# Fit to average structure, save fit coordinates.
reference Avg.rst7.1 [avg]
crdaction crd1 rms ref [avg] :1-330.CA
# Calculate eigenvalues/eigenvectors.
crdaction crd1 matrix covar :1-330.CA name myCovar
runanalysis diagmatrix myCovar out evecs.dat vecs 36 name MyModes
# Project fit coordinates onto eigenvectors.
crdaction crd1 projection P1 modes MyModes beg 1 end 36 :1-330.CA
# Perform clustering using projections.
runanalysis cluster C0 data P1:1-36 crdset crd1 \
hieragglo epsilon 11.5 averagelinkage \
sieve 10 out cnumvtime.dat repout rep repfmt pdb \
summary summary.dat info info.dat cpopvtime cpop.agr normframe \
loadpairdist pairdist CpptrajPairDist \
singlerepout singlerep.nc singlerepfmt netcdf
but with version 15 it not works anymore. I haven't problems with the
prmtop file and tested above script on several trajectories. What was
changed?
The error is:
[reference Avg.rst7.1 [avg]]
Error: reference: Could not set up trajectory.
1 errors encountered reading input.
This is the full output:
CPPTRAJ: Trajectory Analysis. V15.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 09/29/15 01:36:39
| Available memory: 1349.71 MB
Reading '2IOG.prmtop' as Amber Topology
INPUT: Reading Input from file ptraj10.in
[trajin pczn_wt_Final.mdcrd 200 10000000 1]
Reading 'pczn_wt_Final.mdcrd' as Amber Trajectory
Warning: stop 10000000 > #Frames (2500), setting to max.
Warning: Box information present in parm but not in trajectory.
Warning: DISABLING BOX in parm '2IOG.prmtop'!
[rms first :1-330.CA]
RMSD: (:1-330.CA), reference is first frame (:1-330.CA), with fitting.
[average Avg.rst7 restart]
AVERAGE: Averaging over coordinates in mask [*]
Start: 1 Stop: Final frame
Writing averaged coords to file 'Avg.rst7'
[createcrd crd1]
CREATECRD: Saving coordinates from Top 2IOG.prmtop to "crd1"
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: '2IOG.prmtop', 49102 atoms, 15091 res, box: None, 14762 mol, 14748
solvent, 2301 frames
INPUT TRAJECTORIES:
0: 'pczn_wt_Final.mdcrd' is an AMBER trajectory, Parm 2IOG.prmtop
(reading 2301 of 2500)
Coordinate processing will occur on 2301 frames.
TIME: Run Initialization took 0.0001 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '2IOG.prmtop' (3 actions):
0: [rms first :1-330.CA]
Target mask: [:1-330.CA](0)
Warning: No atoms in mask ':1-330.CA'.
Warning: Setup failed for [rms first :1-330.CA]: Skipping
1: [average Avg.rst7 restart]
Averaging over 49102 atoms.
2: [createcrd crd1]
Estimated memory usage (2301 frames): 1.3e+03 MB
----- pczn_wt_Final.mdcrd (200-2500, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 2301 frames and processed 2301 frames.
TIME: Trajectory processing: 50.5465 s
TIME: Avg. throughput= 45.5225 frames / second.
ACTION OUTPUT:
AVERAGE: [Avg.rst7 restart]
Writing 'Avg.rst7' as Amber Restart
'Avg.rst7' is an AMBER restart file, Parm 2IOG.prmtop: Writing 1
frames (1-Last, 1)
DATASETS:
2 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 0
crd1 "crd1" (coordinates), size is 2301 (1293.00 MB) 49102 atoms
---------- RUN END ---------------------------------------------------
[reference Avg.rst7.1 [avg]]
Error: reference: Could not set up trajectory.
1 errors encountered reading input.
TIME: Total execution time: 50.8108 seconds.
Regards,
Filip
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 28 2015 - 16:30:03 PDT
