AMBER Archive (2009)
Subject: Re: [AMBER] problem with amber installation
From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 24 2009 - 05:47:20 CST
the key is the message right at the end of your leap startup: "no
leaprc in search path". you need to copy a leaprc file for the ff that
you want to use into your work directory. look for them in the
dat/leap/cmd directory, and there is lots of info in the archives if
you search for leaprc from the amber web page.
cp /programs/amber9/dat/leap/cmd/leaprc.ff99SB leaprc
On Tue, Feb 24, 2009 at 1:50 AM, nicholus bhattacharjee
> Dear Sir/Madam
> We have purchased the academic licence of amber9 in
> linux platform. We have have succeeded in installing it. The problem is with
> path. We have kept the amber9 folder in /usr/local/.also added the following
> lines in .bashrc file of home folder and source it
> export AMBERHOME=/usr/local/amber9
> export AMBERHOME
> export PATH
> After that when we type the command tleap it shows the following
> -I: Adding /usr/local/amber9/dat/leap/prep to search path.
> -I: Adding /usr/local/amber9/dat/leap/lib to search path.
> -I: Adding /usr/local/amber9/dat/leap/parm to search path.
> -I: Adding /usr/local/amber9/dat/leap/cmd to search path.
> Welcome to LEaP!
> (no leaprc in search path)
> while it should have shown
> -I: Adding /amber/dat/leap/prep to search path.
> -I: Adding /amber/dat/leap/lib to search path.
> -I: Adding /amber/dat/leap/parm to search path.
> -I: Adding /amber/dat/leap/cmd to search path.
> Welcome to LEaP!
> Sourcing leaprc: /amber/dat/leap/cmd/leaprc
> Log file: ./leap.log
> Loading parameters: /amber/dat/leap/parm/parmME.dat
> Loading library: /amber/dat/leap/lib/all_nucleic94.lib
> Loading library: /amber/dat/leap/lib/all_aminoME.lib
> Loading library: /amber/dat/leap/lib/all_aminoctME.lib
> Loading library: /amber/dat/leap/lib/all_aminontME.lib
> Loading library: /amber/dat/leap/lib/ions94.lib
> Loading library: /amber/dat/leap/lib/water.lib
> We are confused about how to source all other files/folders. Please help us.
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> AMBER mailing list
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