Hi,
The 'crdaction' command only pertains to actions. Since 'cluster' is
an analysis, 'crdaction' has no effect. I think what you want is to
use 'crdaction' with 'strip' (so the strip command actually executes
on your input coordinates) and the use 'runanalysis' to run the
clustering, e.g.:
parm native2.parm
loadcrd nat2_md-qm.nc name nat2-0
...
reference nat2_md-qm_0.pdb [ref]
crdaction nat2-0 strip :WAT,QMW,Na+
#Cluster analysis
runanalysis nat2-0 cluster crdset nat2-0 ...
Hope this helps,
-Dan
On Thu, Nov 3, 2016 at 11:59 AM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
> Dear amber users,
>
> I’ve been trying to run a cluster analysis over multiple trajectory files, each one being a portion of the same run. I’ve encountered the following error message:
>
> AMBERHOME/bin/cpptraj -i nat2-0_cluster.in
>
> CPPTRAJ: Trajectory Analysis. V16.16
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 11/03/16 16:42:16
> | Available memory: 1.417 GB
>
> INPUT: Reading input from 'nat2-0_cluster.in'
> [parm native2.parm]
> Reading 'native2.parm' as Amber Topology
> [loadcrd nat2_md-qm.nc name nat2-0]
> Reading 'nat2_md-qm.nc' as Amber NetCDF
> Warning: COORDS data sets do not store times.
> Loading trajectory 'nat2_md-qm.nc' as 'nat2-0'
> .
> .
> .
> [loadcrd nat-ew2-0_mdqm19.nc name nat2-0]
> Reading 'nat-ew2-0_mdqm19.nc' as Amber NetCDF
> Appending trajectory 'nat-ew2-0_mdqm19.nc' to COORDS data set 'nat2-0'
> ----- nat-ew2-0_mdqm19.nc (1-250, 1) -----
> [reference nat2_md-qm_0.pdb [ref]]
> Reading 'nat2_md-qm_0.pdb' as PDB
> Read CRYST1 info from PDB: a=62.134 b=62.134 c=62.134 alpha=109.47 beta=109.47 gamma=109.47
> Warning: Low precision truncated octahedron angles detected (109.47 vs 109.471).
> Warning: If desired, the 'box' command can be used during processing
> Warning: to set higher-precision angles.
> Read CRYST1 info from PDB: a=62.134 b=62.134 c=62.134 alpha=109.47 beta=109.47 gamma=109.47
> Setting active reference for distance-based masks: 'nat2_md-qm_0.pdb'
> [strip :WAT,QMW,Na+]
> Warning: Action specified before trajin/ensemble. Assuming trajin.
> STRIP: Stripping atoms in mask [:WAT,QMW,Na+]
> [crdaction nat2-0 cluster crdset nat2-0 dbscan minpoints 5 epsilon 0.9 sievetoframe rms :32,35,179&!.H= reference mass sieve 10 random out nat_clst-vs-t.dat summary nat_clst-sum.dat info nat_clst-info.dat cpopvtime nat_cpop-vs-t.agr normframe repout nat_rep repfmt pdb ]
> Using set 'nat2-0'
> ----- nat2-0 (1-5250, 1) -----
> 'cluster': Command not found.
> 1 errors encountered reading input.
> TIME: Total execution time: 5.4636 seconds.
> Error: Error(s) occurred during execution.
>
> Here is the input file:
>
> #Load topology and trajectories
> parm native2.parm
> loadcrd nat2_md-qm.nc name nat2-0
> loadcrd nat-ew2-0_mdqm.nc name nat2-0
> loadcrd nat-ew2-0_mdqm1.nc name nat2-0
> loadcrd nat-ew2-0_mdqm2.nc name nat2-0
> loadcrd nat-ew2-0_mdqm3.nc name nat2-0
> loadcrd nat-ew2-0_mdqm4.nc name nat2-0
> loadcrd nat-ew2-0_mdqm5.nc name nat2-0
> loadcrd nat-ew2-0_mdqm6.nc name nat2-0
> loadcrd nat-ew2-0_mdqm7.nc name nat2-0
> loadcrd nat-ew2-0_mdqm8.nc name nat2-0
> loadcrd nat-ew2-0_mdqm9.nc name nat2-0
> loadcrd nat-ew2-0_mdqm10.nc name nat2-0
> loadcrd nat-ew2-0_mdqm11.nc name nat2-0
> loadcrd nat-ew2-0_mdqm12.nc name nat2-0
> loadcrd nat-ew2-0_mdqm13.nc name nat2-0
> loadcrd nat-ew2-0_mdqm14.nc name nat2-0
> loadcrd nat-ew2-0_mdqm15.nc name nat2-0
> loadcrd nat-ew2-0_mdqm16.nc name nat2-0
> loadcrd nat-ew2-0_mdqm17.nc name nat2-0
> loadcrd nat-ew2-0_mdqm18.nc name nat2-0
> loadcrd nat-ew2-0_mdqm19.nc name nat2-0
> reference nat2_md-qm_0.pdb [ref]
> strip :WAT,QMW,Na+
> #Cluster analysis
> crdaction nat2-0 cluster crdset nat2-0 \
> dbscan minpoints 5 epsilon 0.9 sievetoframe \
> rms :32,35,179&!.H= reference mass \
> sieve 10 random \
> out nat_clst-vs-t.dat \
> summary nat_clst-sum.dat \
> info nat_clst-info.dat \
> cpopvtime nat_cpop-vs-t.agr normframe \
> repout nat_rep repfmt pdb \
>
> I wonder if it could be due to the fact that Amber & AmberTools 16 have been installed in serial only (?)
> Also, as I’ve never run this kind of analysis, I wonder if there is any mistake in my input file?
>
> Thanks for any suggestion,
>
> Sincerely,
>
> Ruth
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Nov 03 2016 - 19:00:02 PDT
