[AMBER] Fwd: Running PCA

From: Nicole Ippolito <ippolito.nicole89.gmail.com>
Date: Tue, 29 Jul 2014 08:24:45 -0500

Hello AMBER users,

I am trying to get the percent occupancy using cpptraj but I am getting an
error. There seems to be a problem reading my input file. Below is my
trajin file and below that is the error file.

Thank you for your help,

Nicole

trajin ~/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz
createcrd crd1
run
rms first .CA
reference V600E505H_sor_aMD_avg_pdb.pdb
crdaction crd1 rms reference .CA
crdaction crd1 matrix out matrix.dat name mymatrix covar .CA
runanalysis diagmatrix mymatrix out evecs.dat vecs 20 name mymodes
crdaction crd1 projection modes evecs.dat start 1 stop 3 .CA myproj
hist myproj:1 bins 200 out PC.hist.agr
hist myproj:2 bins 200 out PC.hist.agr


CPPTRAJ: Trajectory Analysis. V14.01
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_
        Reading 'parm' as Amber Topology
INPUT: Reading Input from STDIN
  [trajin ~/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz ]
        Reading
'/home/aubndi/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz' as
Amber Trajectory
  [createcrd crd1 ]
    CREATECRD: Saving coordinates from Top parm to "crd1"
  [run]
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: 'parm', 36610 atoms, 11002 res, box: Orthogonal, 10731 mol, 10722
solvent, 60000 frames

INPUT TRAJECTORIES:
 0: 'V600E505H_sor_aMD_0_300ns.crd.gz' is an AMBER trajectory, Parm parm
(Orthogonal box) (reading 60000 of 60000)
  Coordinate processing will occur on 60000 frames.
TIME: Run Initialization took 0.0000 seconds.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'parm' (1 actions):
  0: [createcrd crd1 ]
----- V600E505H_sor_aMD_0_300ns.crd.gz (1-60000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Error: reference: Could not set up
trajectory.
        1 errors encountered reading input.
100% Complete.

Read 60000 frames and processed 60000 frames.
TIME: Trajectory processing: 1743.3814 s
TIME: Avg. throughput= 34.4159 frames / second.

ACTION OUTPUT:

DATASETS:
  1 data set:
        crd1 "crd1" (coordinates), size is 60000 (25138 MB) Box Coords,
36610 atoms
---------- RUN END ---------------------------------------------------
  [rms first .CA]
    RMSD: (.CA), reference is first frame (.CA), with fitting.
  [reference V600E505H_sor_aMD_avg_pdb.pdb]
TIME: Total execution time: 1743.8619 seconds.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 29 2014 - 06:30:03 PDT
Custom Search