Re: [AMBER] clustering in PC subspace

From: filip fratev <fratev.biomed.bas.bg>
Date: Tue, 29 Sep 2015 02:10:18 +0300

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 - 16:30:03 PDT
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