AMBER Archive (2009)

Subject: RE: [AMBER] ptraj - cluster

From: Cihan Aydin (
Date: Fri Jul 17 2009 - 09:22:37 CDT

Hey Wei,

I looked at the AmberTools manual but apart from (5.1) there was no
reference to the 2drms command and no description of the syntax.

A google search turned this...

2drms [out filename] [raw | ps | plotmtv] [mass] [mask]

Calculate a 2D RMS plot for the atoms specified, dumping the output to
one of the specified file formats.

My question here is why not this command is apparent in the manual? Is
it obsolete or it was missed? My second question is that can this matrix
used as an input to the ptraj clustering utility?



p.s. Aydin is my surname

On Fri, 2009-07-17 at 07:34 -0500, Wei Huang wrote:
> Hi Aydin,
> Is the "2drms" what you need?
> Cheers,
> Wei
> -----Original Message-----
> From: [] On Behalf
> Of Cihan Aydin
> Sent: Thursday, July 16, 2009 12:55 AM
> To: AMBER Mailing List
> Subject: [AMBER] ptraj - cluster
> Greetings,
> I have a small question. Is it possible to just get the RMSD matrix for
> all frames and just quit without going through the clustering?
> Thanks,

Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student @ Schiffer Lab

364 Plantation St. LRB 970M Worcester, MA 01605 +1 (508) 856-3430

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