Hi,
On Mon, Sep 28, 2015 at 5:17 PM, filip fratev <fratev.biomed.bas.bg> wrote:
> 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?
This is an unintended consequence of "average" now behaving like the
rest of cpptraj, i.e. when a single restart frame is to be printed the
numerical '.X' suffix is omitted ('trajout'/'outtraj' in cpptraj has
behaved like this since version 12). Sorry for the minor headache but
glad you were able to quickly find a workaround.
Note that in your first script your atoms masks are malformed. This is
evidenced by some of the warnings that cpptraj emits, e.g.:
Warning: No atoms in mask ':1-330.CA'.
Warning: Setup failed for [rms first :1-330.CA]: Skipping
The period characters '.' should be '@'. It seems like you corrected
this in the next script you posted but I wanted to point it out just
in case.
FYI, you now no longer need to write the averaged coordinates to disk;
they can be saved as a COORDS data set and used directly as a
reference structure via the 'crdset' keyword, e.g.
# Average the trajectory.
rms first :
1-330.CA
average crdset AVG
createcrd crd1
run
# Fit to average structure, save fit coordinates.
crdaction crd1 rms ref AVG :
1-330.CA
...
Hope this helps,
-Dan
>
> 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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--
-------------------------
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Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
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Received on Mon Sep 28 2015 - 20:30:03 PDT
