Hi Dan,
Thanks a lot for your answer, it is working now!
Ruth
> On 04 Nov 2016, at 02:41, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> 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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>
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Received on Fri Nov 04 2016 - 02:00:03 PDT
