AMBER Archive (2009)

Subject: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Fri Dec 04 2009 - 03:55:05 CST

Dear Amber users,
I am trying to perform so called relxed complex scheme and I need the clustering of protein conformations from MD trajectory for it.
The full procedure is listed here: https://www.nbcr.net/pub/wiki/index.php?title=Relaxed_Complex_Scheme,_Part_I:_Molecular_Dynamics_and_Clustering

But I have questions on running cluster procedure of ptraj.

The ptraj clustering command format is listed on that web site:

cluster out filename [representative format] [average format] [all format] algorithm ([clusters n] | [epsilon critical_distance])
[rms|dme] [sieve s [start start_frame | random]] [verbose verb] [mass] mask

then the exact example ptraj file is listed:

"* Start with cluster=1
trajin N1-apo-all-CA-aligned.dcd
cluster out avg-1 representative none average none all none averagelinkage clusters 1 mass rms
"(:35-37 | :51-56 | :64-70 | :74 | :97-98 | :114-118 | :141-146 | :161-165 | :195-196 | :211 | :213 | :262-265 | :286 | :319-320 |
:344-359) & @CA,C,N,O"
go"

In my case I have made the next ptraj file:

trajin fzd2_w_md5.mdcrd
cluster out avg-1 representative none average none all none averagelinkage clusters 1 mass rms
"(:1-240) & @CA,C,N,O"
go

but I don't know what file to specify as output? .rst, .pdb or .mdcrd formats for clustered conormations don't work.
 I also wonder about more detailed meaning of the flags in cluster command, like the representative structure - this is representative word after cluster command?

I use then ptraj protein.prmtop cluster .ptraj "some output file which I don't know"

I haven't found information on this in Amber10 or Amber9 manuals.

Best regards,
Andrew

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