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.
for example:
cp /programs/amber9/dat/leap/cmd/leaprc.ff99SB leaprc

On Tue, Feb 24, 2009 at 1:50 AM, nicholus bhattacharjee
<nicholusbhattacharjee_at_gmail.com> wrote:
> 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
> PATH=$PATH:$AMBERHOME/exe:$
> AMBERHOME/dat/leap/:$AMBERHOME/dat/leap/lib::$AMBERHOME/dat/leap/parm:$AMBERHOME/dat/leap/cmd
> 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
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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