[AMBER] How to do clustering analysis by ptraj?

From: Biao Ma <jackyma1981.gmail.com>
Date: Tue, 17 Sep 2013 16:43:33 +0900

Dear amber users.

I have some question to ask.
Q1:
I want to do the clustering analysis refer to this paper(
http://pubs.acs.org/doi/abs/10.1021/jp208433w).
a part of the method from above paper:
*Simulated **trajectories were clustered into distinct groups based on
average*
*linkage methods by ptraj. Based on the main-chain rmsd, each*
*snapshot is compared against the average coordinates of the*
*existing groups after rigid-body alignment. A snapshot may*
*become a member of its closest cluster if the rmsd is smaller*
*than a given cutoff (3 ). Otherwise, a new cluster would be*
*generated if the minimum rmsd exceeded the cutoff.*

My trajectories were produced by REMD, I pick up the trajectories of 340.8K
and write the ptraj input file as follow:

trajin ../remd.340.8k.binpos
cluster out cluster all Amber representative pdb average pdb averagelinkage
epsilon 3.0 rms :2-103.CA

Now I want to get some advice about whether this input file will do the
same analysis to the paper.

Q2:
I finished the ptraj cluster analysis, use the above input file.
The whole process is used about 20 days.
computer info:
Linux CentOS 5
Intel(R) Xeon(R) CPU E5472 . 3.00GHz
MemTotal: 16434952 kB
( *Why spend so long time ?*)

I found that some PDB file can not be saved( *What is the reason, and
whether it has some effect of the analysis result?*)
I checked there are only 1019 cluster.rep.c* and cluster.avg.c* files saved.

The part log file of ptraj:
Successfully completed.

Resource usage summary:

    CPU time :1730738.50 sec.

The output (if any) follows:


  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 12.0 integrated" (4/2012)
  -/- Executable is: "ptraj"
  /-\ Running on 1 processor(s)
  \-/ Residue labels:
......

Too many clusters, clusters beyond 62 will be represented using *.
ptrajOutputCoordinates(): Could not write PDB file cluster.rep.c1019
ptrajOutputCoordinates(): Could not write PDB file cluster.avg.c1019
WARNING in ptrajOutputCoordinates(): Error opening
output coordinate file (cluster.c1020)
ptrajOutputCoordinates(): Could not write PDB file cluster.rep.c1020
ptrajOutputCoordinates(): Could not write PDB file cluster.avg.c1020
ptrajOutputCoordinates(): Could not write PDB file cluster.rep.c1021
ptrajOutputCoordinates(): Could not write PDB file cluster.avg.c1021
ptrajOutputCoordinates(): Could not write PDB file cluster.rep.c1022
ptrajOutputCoordinates(): Could not write PDB file cluster.avg.c1022
ptrajOutputCoordinates(): Could not write PDB file cluster.rep.c1023
ptrajOutputCoordinates(): Could not write PDB file cluster.avg.c1023

I attach the log file of ptraj.

Q3:
There are some files produced,
CluseterMerging.txt
cluster.txt
cluster.rep.c1-1019
cluster.avg.c1-1019

How should I use this files to get the best populated cluster and
represented PDB file?

Waiting for your valuable reply.

Thanks a lot.

Biao Ma


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Received on Tue Sep 17 2013 - 01:00:02 PDT
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