Dear Dr. Daniel,
Thanks for your comments, please find my response below.
On Thu, Oct 4, 2012 at 8:05 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Thu, Oct 4, 2012 at 2:28 AM, vaibhav dixit <vaibhavadixit.gmail.com>
> wrote:
> > Is there any flag in the cluster command to specify this file, I can't
> see
> > it in the AmberTools, Amber manual.
>
> As far as I know the file name is hard-coded to PairwiseDistances. Why
> not just soft-link the file to the directory you intend to run
> clustering, e.g.:
>
> cd <target directory>
> ln -s <source-pairwise-distance-location> .
>
> This suggestion has worked and I'm able to make the program read the
PairwiseDistance file from other folder.
> > Can I run all the jobs from one ptraj input file, if so how? I tried
> this:
>
> Yes you should be able to. Are you sure you aren't getting any errors?
> Are you able to run the commands separately?
>
> Yes I'm able to run the commands separately, without any errors. But when
I put two cluster commands one below the other I did not get any output
from the first command, even though on the terminal it showed to have
finished applying the clustering algorithm. It also shows that second
cluster command is clustering the data. I expected more output on the
screen and PDB files in the folder. I doubt if it is rerunning the
clustering is it?
-------
Processing AMBER trajectory file
/home/gncp/Documents/MD/PPAR_MD_study/BVT13/2Q6S_BVT_md_100ns_VAC.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
The first pass through the trajectory is complete.
Read in the existing PairwiseDistances file
Clustering using the average linkage algorithm.
Aligning the most representative frames from each clusters to cluster 4.
The first pass through the trajectory is complete.
Read in the existing PairwiseDistances file
Clustering using the average linkage algorithm.
^C
---------------
-Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Thu Oct 04 2012 - 22:30:02 PDT
