AMBER Archive (2007)

Subject: Re: AMBER: amber9/mmtsb

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Dec 18 2007 - 11:15:55 CST

Professor Case:
>From your answer I fear I am just wasting your time. From tutorial B3:

"In order to complete this section of the tutorial you will require the MMTSB
toolset. This is not part of AMBER but can be downloaded free of charge from
http://mmtsb.scripps.edu/software/mmtsbtoolset.html. If you are running this
tutorial at an AMBER workshop then the MMTSB toolset should already be
installed on your machine. You can check by seeing if the environment variable
MMTSBDIR is set. E.g.

>echo $MMTSBDIR

If it isn't set then you probably need to install the MMTSB toolset. Refer to
the documentation on the website. Essentially you should untar the toolset to
somewhere like /usr/local/mmtsb, set MMTSBDIR to this directory and then add
$MMTSBDIR/bin and $MMTSBDIR/perl to your path."

The given web site tells about requirements:

"The MMTSB Tool Set consists of Perl5 packages, Perl5 programs that use the
packages and provide user interfaces, as well as some C, C++, and FORTRAN
programs for more compute-intensive functions.
For installation of the Tool Set perl version 5.004 or newer and C, C++, and
Fortran compilers are required. Gnu compilers can be downloaded for most
platforms if necessary. Binary packages with precompiled executables are not
available at this time.
The Tool Set is intended to be installed as a complete distribution package.
Single components usually depend on other components in the Tool Set and may
not be functional if separated from the distribution...........Without CHARMM
the functionality of the Tool Set is limited for the most part to lattice-based
low-resolution modeling."

>From there my original question, i.e., what happens if perl is alredy installed
as Debian package, and what happens if Amber 9 is installed instead of CHARMM.

I fear I misunderstood a lot. Though, I had to explain why I posted.

Thanks
francesco

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Tue, Dec 18, 2007, Francesco Pietra wrote:
>
> > On looking for the way to carry out cluster analysis (of the type of
> > tutorial B3) with Amber 9, I was unable to find documentation for MMTSB in
> > combination with Amber 9. Amber proposes a patch for Amber 8, while the
> > MMTSB web site only refers to CHARMM. Should Amber 9 be recompiled with
> > MMTSB?
>
> I don't understand: the clustering in mmtsb just uses pdb files as inputs.
> It shouldn't matter where the pdb files come from: amber 8 or amber 9, or
> charmm.
>
> What happened when you did your clustering using Amber 9?
>
> ...dac
>
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