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.
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Received on Fri Jul 25 2014 - 11:00:02 PDT
