AMBER Archive (2008)

Subject: Re: AMBER: Install problems

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Sep 09 2008 - 06:37:16 CDT

On Mon, Sep 08, 2008, Mark Williamson wrote:
>
> Reading the mailing list over the past few years, I think generally new
> AMBER users fall down on:
>
> a) Not having other bits of software that AMBER needs to build installed.
> b) Installation of 3rd party compilers (such as ifort) that support
> the Fortran 95 (F95) standard since the "free" GNU compilers do not
> support this yet...

Just a note: current versions of the free GNU compilers (both gfortran and
g95) work fine for Amber (at least in my hands). The code they generate is
not quite as fast as that from ifort, but that only becomes important when
doing long calculations.

My general recommendation for "new AMBER users" (which is what Mark is
suggesting as well) is to use gfortran, which is simple to install and
configure. If you later find that Amber suits your needs, and want to run
long simulations, then you can consider installing other compilers. At that
point, you will (a) have more experience, which often makes tracking down
problems easier; (b) have a reference working installation, so that you can
more easily check the new compiles.

Thanks to Mark for providing the detailed instructions.

>
> 9) There is an issue with the MOPAC wrapper script that will cause it to
> fail with Ubuntu's default /bin/sh (dash). Fix it by telling it to use bash:

??? Do you know what the problem is with dash? This is about as simple
a shell script as one could come across, so what is failing?

...thx...dac

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