In fact, when I replaced Avg.rst7.1 [avg] with Avg.rst7 [avg] it works
but this is strange and would affect many other scripts?
Regards,
Filip
На 29-Sep-15 в 02:10, filip fratev написа:
> 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
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Received on Mon Sep 28 2015 - 16:30:05 PDT
