AMBER Archive (2009)

Subject: Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Mon Oct 19 2009 - 16:44:42 CDT

Hi Jianjin and Tec3!
 
I guess I figured out what went wrong.
Here is the head of ptraj output which tells me the reason why I kept getting an error message with the cluster function.

  -/-   PTRAJ: a utility for processing trajectory files
  /-\ 
  \-/   Version: "AMBER 9.0 integrated" (April 2006)
 
I victimized myself with the ptraj module of AMBERv9 that is installed on my older laptop. I thought I had ptraj 10 on that laptop..
 
I re-tried Tec3's command line below on the ptraj module of AMBERv10 at the Turkish GRID infrastructure and this time it worked out just fine..
 
thank you  all..
 
regards,
 
Jenk  

--- On Mon, 10/19/09, Jianyin Shao <jyshao2004_at_gmail.com> wrote:

From: Jianyin Shao <jyshao2004_at_gmail.com>
Subject: Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Monday, October 19, 2009, 1:16 PM

Hi,  Jenk,

Would you please send me the information printed by ptraj prior to the
segmentation fault?

Jianyin

On Sat, Oct 17, 2009 at 1:02 AM, Cenk (Jenk) Andac <cenk_andac_at_yahoo.com>wrote:

>
>
> Hi Tec3,
>
> Unfortunately I keep getting the same error message "Segmentation fault"
>  with the command line below
>
> cluster out clusters/c20ns all amber representative pdb average pdb \
>   averagelinkage sieve 10 clusters 10 rms :1-39
>
> I don't know why.
>
> Jenk
>
> --- On Fri, 10/16/09, Thomas Cheatham III <tec3_at_utah.edu> wrote:
>
>
> From: Thomas Cheatham III <tec3_at_utah.edu>
> Subject: Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Friday, October 16, 2009, 10:33 AM
>
>
>
> > I have been working on a non-competitive enzyme reaction in explicit
> ...
> > clusters.However, I can't seem to get the ptraj's cluster function
> > working as it appears below:
>
> > trajin enzyme.qmmm.traj
> > cluster out reductase representative pdb average pdb means clusters 5 rms
> :1-84
>
> I will look into why it is core dumping, but you need to specify an
> algorithm for the clustering....  There are many, each with different
> characteristics and you will see that each creates different clusters for
> MD trajectory data; see for example Shao et al., JCTC 3, 2312 (2007).
>
> Here is what I use (the sieve is useful is you have lots of frames):
>
> cluster out clusters/c20ns all amber representative pdb average pdb \
>   averagelinkage sieve 10 clusters 10 rms :1-39
>
> --tec3
> -----Inline Attachment Follows-----
>
>
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