AMBER Archive (2007)

Subject: Re: AMBER: Fails to load libraries present in /leap/lib/

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 09 2007 - 12:25:41 CDT

On Mon, Apr 09, 2007, Neelanjana Sengupta wrote:
>
> In the first AMBER-workshop tutorial (DNA polyA-polyT), when I do:
>
> $AMBERHOME/exe/teLeap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99 , I get:
>
> Loading parameters: ./parm99.dat
> Loading library: ./all_nucleic94.lib
> Loading library: ./all_amino94.lib
> Could not open file all_aminoct94.lib: not found
> Could not open database: all_aminoct94.lib
> Could not open file all_aminont94.lib: not found
> Could not open database: all_aminont94.lib
> Loading library: ./ions94.lib
> Loading library: ./solvents.lib

What directory are you in when you run this command? It looks like it is
loading parm99.dat, etc. from the current directory ("Loading parameters:
./parm99.dat"), but not finding all_aminoct94.lib in the current directory.

I don't think the Amber 7 understands how to automatically look in the right
place for all the libraries...using leaprc files in this way comes with later
versions of the code. You may have to edit your tleap script to enter the
proper path variables for you machine.

...good luck...dac

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