Re: [AMBER] Clustering logistics

From: Daniel Roe <>
Date: Mon, 24 Feb 2020 12:59:02 -0500


On Mon, Feb 24, 2020 at 12:27 PM Debarati DasGupta
<> wrote:
> All I need to know is what are the results I am expecting once I do a cpptraj command line on my input file. I do not want to run it as a black box. ( I have opted DBSCAN just randomly, please suggest if its not appropriate and any specific algorithms I may be needing to use)

If I could tell you that, there would be no reason to have cpptraj :-).

Seriously though, your best bet here is to just make sure you
understand what input you are providing cpptraj with (i.e. read the
manual entries for each command and keyword you are using), and
actually look at the output messages that cpptraj produces - pay
special attention to anything starting with 'Warning:' or 'Error:'.
Lastly, as when running all things for the first time, trying a small
subset of your data (ideally something that will complete in less than
1 minute) is recommended so you can get an idea for what output is
produced, run timing, etc. This will also help you catch annoying
problems that will waste your time if tried on the larger set of data.

Unfortunately clustering is very much an art form, not a science, so
be prepared for a lot of trial and error. And of course, if you
haven't already, I highly recommend you read the *best* paper on
clustering of MD trajectory data by Shao, Cheatham et al:


> Thank you all.
> parm 2XXX_solvated.prmtop
> trajin 2XXX_prod1.mdcrd 1 100000 10
> ###we are worried about protein conformations, and hence we don’t need to bother about solvents and ions during the clustering procedure!
> strip :Cl-,Na+,WAT
> center mass origin :1-152
> image origin center
> #Align trajectory to reference structure by minimizing RMSD
> reference 2XXX_imaged_run1.pdb
> rms reference mass out RMSD_CA.txt :2-151.CA,C,N
> cluster cluster_out dbscan minpoints 20 epsilon 1 rms :2-151.CA,C,N out combined.dat summary summary.out info data_run1_water_cluster singlerepout clusters.pdb singlerepfmt pdb
> go
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Received on Mon Feb 24 2020 - 10:00:01 PST
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