Dear Michael,
I'd suggest to use a line like
rms :111.OG,:164.NE2 \
for a working mask, as this type works for pure rms fits as well. (See
section 29.2.2 of the Amber16 manual about the details of the masks in
cpptraj.)
I'm not sure, however, whether this cluster command suits your intention
about the analysis, but I'm not an expert there.
Regards,
Anselm
Am 12.05.2016 13:12, schrieb Michael Shokhen:
> Dear Anselm,
>
> Thank you for your response where you suggested that
> "your mask of the rms argument is broken as it contains spaces
> thus the second part of your mask ':164.NE2' is mistakenly interpreted
> as a further argument."
>
> Unfortunately, you didn't present a correct form of the command.
> I would highly appreciate if you will send me a correct variant of the
> line:
> rms :111.OG, :164.NE2 \
>
> Thank you,
> Michael
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il
>
> ________________________________________
> From: Dr. Anselm Horn <anselm.horn.fau.de>
> Sent: Thursday, May 12, 2016 1:28:29 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error in cluster analysis by cpptraj
>
> Dear Michael,
>
> probably your mask of the rms argument is broken as it contains spaces;
> thus the second part of your mask ':164.NE2' is mistakenly interpreted
> as a further argument.
> Correcting the mask string may help solve the problem.
>
> Regards,
>
> Anselm
>
>
>
>
> Am 12.05.2016 12:06, schrieb Michael Shokhen:
>> Dear Amber experts,
>>
>>
>> I need to conduct cluster analysis of several sequential MD trajectories
>>
>> by inter atomic bond distance :111.OG, :164.NE2
>>
>>
>> I never used previously such analysis, so
>>
>> cpptraj reported about ERROR.
>>
>>
>> I need your advise to identify error in my cpptraj.combined.cluster.in input file
>>
>> that I ran by the command:
>>
>> $ cpptraj -i cpptraj.combined.cluster.in
>>
>>
>> See details below.
>>
>>
>> Thank you,
>>
>> Michael
>>
>> cpptraj.combined.cluster.in file:
>>
>> # Combined cluster analysis with cpptraj.
>>
>> # Load topology and both trajectories
>> parm ../*.prmtop
>> trajin ../20_/prod4.mdcrd # 5000 frames
>> trajin ../21_/prod5.mdcrd # 5000 frames
>> trajin ../22_/prod6.mdcrd # 4971 frames
>> # Remove ions so they do not appear in output structures.
>> strip :WAT,Cl-,Na+,OL,PA,PE
>> # Cluster analysis command
>> # C1: Cluster output data set(s) name.
>> # dbscan: Clustering algorithm.
>> # minpoints: Minimum # of points to form a cluster.
>> # epsilon: Distance cutoff for forming cluster.
>> # sievetoframe: Restore sieved frames by comparing to all cluster frames,
>> # not just centroid.
>> # rms <mask>: Use RMSD of atoms in <mask> as distance metric.
>> # sieve 20: Use <total> / 20 initial frames for clustering.
>> # out <file>: Write cluster number versus time to file.
>> # info <file>: Write detailed cluster results (including DBI, pSF etc) to file.
>> # summarysplit <file>: Write cluster information for split to file.
>> # splitframe 5000: Split clustering at frame 5000 (where first traj stops).
>> cluster C1 \
>> dbscan minpoints 25 epsilon 0.9 sievetoframe \
>> rms :111.OG, :164.NE2 \
>> sieve 20 \
>> out combined.cnumvtime.dat \
>> info combined.info.dat \
>> summarysplit split.dat splitframe 5000
>>
>>
>> The result:
>>
>> $ cpptraj -i cpptraj.combined.cluster.in
>>
>> CPPTRAJ: Trajectory Analysis. V15.00
>> ___ ___ ___ ___
>> | \/ | \/ | \/ |
>> _|_/\_|_/\_|_/\_|_
>>
>> | Date/time: 05/12/16 12:50:09
>> | Available memory: 170.02 MB
>>
>> INPUT: Reading Input from file cpptraj.combined.cluster.in
>> [parm ../*.prmtop]
>> Reading '../mc.prmtop' as Amber Topology
>> [trajin ../20_/prod4.mdcrd ]
>> Reading '../20_/prod4.mdcrd' as Amber NetCDF
>> [trajin ../21_/prod5.mdcrd ]
>> Reading '../21_/prod5.mdcrd' as Amber NetCDF
>> [trajin ../22_/prod6.mdcrd ]
>> Reading '../22_/prod6.mdcrd' as Amber NetCDF
>> [strip :WAT,Cl-,Na+,OL,PA,PE]
>> STRIP: Stripping atoms in mask [:WAT,Cl-,Na+,OL,PA,PE]
>> [cluster C1 dbscan minpoints 25 epsilon 0.9 sievetoframe rms :111.OG, :164.NE2 sieve 20 out combined.cnumvtime.dat info combined.info.dat summarysplit split.dat splitframe 5000]
>> CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:111.OG,]) best-fit
>> DBSCAN:
>> Minimum pts to form cluster= 25
>> Cluster distance criterion= 0.900
>> Sieved frames will only be added back if they are within
>> 0.900 of a frame in an existing cluster.
>> (This option is more accurate and will identify sieved
>> frames as noise but is slower.)
>> Initial clustering sieve value is 20 frames.
>> Cluster # vs time will be written to combined.cnumvtime.dat
>> Cluster information will be written to combined.info.dat
>> Summary comparing parts of trajectory data for clusters will be written to split.dat
>> Frames will be split at: 5000
>> Error: [cluster] Not all arguments handled: [ :164.NE2 ]
>> 1 errors encountered reading input.
>> TIME: Total execution time: 0.1955 seconds.
>>
>>
>>
>>
>>
>> *****************************
>> Michael Shokhen, PhD
>> Associate Professor
>> Department of Chemistry
>> Bar Ilan University,
>> Ramat Gan, 52900
>> Israel
>> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
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Received on Thu May 12 2016 - 05:30:03 PDT
