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>
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>
>
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Received on Thu May 12 2016 - 04:30:04 PDT
