AMBER Archive (2009)

Subject: Re: [AMBER] problem with amber installation

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Tue Feb 24 2009 - 22:29:11 CST

Dear sir/madam
                      I have copied leaprc.ff99SB as leaprc in my working
directory. the tleap is working fine. but i can not use the solvateBox mol
WATBOX216 10. its showing massage as bellow

solvateBox: Argument #2 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]

what else do i have to copy to my working directory. the tutorial provided
with the amber9 cd does not tell everything in details. please help. thanx
in advance.

On Tue, Feb 24, 2009 at 5:17 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> 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
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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