Thanks Dan,
Apparently cpptraj ignored the forward slash and didn't read the whole command. Problem solved.
gard
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Friday, April 10, 2015 1:29 PM
To: AMBER Mailing List
Subject: Re: [AMBER] cpptraj write data from runanalysis
Hi,
On Fri, Apr 10, 2015 at 12:29 PM, Gard Nelson <Gard.Nelson.nantbio.com> wrote:
> I'm trying to figure out how to get cpptraj to write all of the output from a clustering calculation.
>
> runanalysis cluster C data P:1-30 crdset crds \
> hieragglo clusters 20 averagelinkage \
> rms :13-18,31-37,59-72 sieve 10 random \
> out out.dat \
> summary summary.dat \
> info info.dat \
> summaryhalf part.dat \
>
> When I run just this, most of the info I'd normally see in the "info" file is written to the screen.
This indicates something went wrong with you input, since the default more for the cluster info file is to print to STDOUT when no file name specified. You should post your entire input, and examine your cpptraj output for any errors/warnings - in particular make sure cpptraj was able read the input line correctly. You'll be able to tell because you should see the parsed input line right before the command output,
e.g.:
CLUSTER: Using coords dataset crds, clustering using RMSD (mask
[:13-18,31-37,59-72]) best-fit
Hierarchical Agglomerative: 20 clusters, average-linkage.
Initial clustering will be randomly sieved (with value 10).
Cluster # vs time will be written to out.dat
Cluster information will be written to info.dat
Summary of cluster results will be written to summary.dat ...
-Dan
PS - The only data sets generated by 'cluster' in cpptraj are the cluster number vs time (named C in your input) and cluster population vs time if cpopvtime specified (which would be named C[Pop]:X if it were specified in your input).
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Apr 10 2015 - 15:30:05 PDT
