Hi,
You're missing some elements from your script, and have a few things out of
order. By default in cpptraj when you specify an action or an analysis it
goes into either the action list or analysis list respectively; it is not
immediately executed. I will go through your input and try to explain
what's happening:
On Fri, Jul 25, 2014 at 11:56 AM, Nicole Ippolito <
ippolito.nicole89.gmail.com> wrote:
> trajin ~/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz
> createcrd crd1
> run
>
Here you are essentially loading a trajectory into the coords data set
named 'crd1'. The 'run' statement means "process all currently loaded
trajectories with any initialized actions", and 'createcrd' is the only
action set up here.
> rms first .CA
> reference V600E505H_sor_aMD_avg_pdb.pdb
>
These statements seem out of order. They are placed after the run
statement, and so they are not processed until the first 'run' is
completed. Presumably your intent was to remove overall rotation and
translation from your coordinates with the 'rms' statement. If that is the
case then it should come before the createcrd statement. Also, since you
also have a later 'rms' command that fits to a reference, this makes me
think this first 'rms' was for creating an average structure to use as a
reference, and the 'average' command is missing.
The 'reference' command is actually what kills the run: if you check your
output you will see the message "Error: reference: Could not set up
trajectory". This indicates that "V600E505H_sor_aMD_avg_pdb.pdb" does not
exist; perhaps you meant to create an average?
> 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
>
These statements seem fine as long as a reference is successfully loaded
and your 'crd1' coordinates is properly loaded.
> crdaction crd1 projection modes evecs.dat start 1 stop 3 .CA myproj
>
This will not work, since you named your modes internally as 'mymodes' but
you're trying to use the file name 'evecs.dat'. Change 'evecs.dat' to
'mymodes'.
> hist myproj:1 bins 200 out PC.hist.agr
> hist myproj:2 bins 200 out PC.hist.agr
>
This seems like it should work as well.
So to summarize, your final script should look something like this:
trajin ~/BRAF/MD/V600E505H/sor/V600E505H_sor_aMD_0_300ns.crd.gz
# Fit to first frame for averaging
rms first .CA
# Average the trajectory
average V600E505H_sor_aMD_avg_pdb.pdb pdb
# Save the rms-fit coords
createcrd crd1
# First run
run
# Load the generated average as reference
reference V600E505H_sor_aMD_avg_pdb.pdb
# Fit saved coords to the reference
crdaction crd1 rms reference .CA
# Calculate covariance matrix from fit coords
crdaction crd1 matrix out matrix.dat name mymatrix covar .CA
# Diagonalize matrix to get eigenvectors/eigenvalues
runanalysis diagmatrix mymatrix out evecs.dat vecs 20 name mymodes
# Project fit coords along eigenvectors 1-3
crdaction crd1 projection modes evecs.dat start 1 stop 3 .CA myproj
# Set up histograms for PC projections
hist myproj:1 bins 200 out PC.hist.agr
hist myproj:2 bins 200 out PC.hist.agr
hist myproj:3 bins 200 out PC.hist.agr
# Run analyses
runanalysis
Note that the final 'runanalysis' is not strictly necessary as cpptraj will
try to run any actions or analyses that are set up before quitting when
reading a script, but I include it for completeness.
Hope this helps,
-Dan
>
>
> 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
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jul 29 2014 - 07:30:03 PDT
