AMBER Archive (2009)

Subject: Re: [AMBER] problem with amber installation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 25 2009 - 05:25:34 CST

we can't help since you did not tell us what you used for your leap input.

On Tue, Feb 24, 2009 at 11:29 PM, nicholus bhattacharjee
<nicholusbhattacharjee_at_gmail.com> wrote:
> 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
>> >
>>
>> _______________________________________________
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>>
>
>
>
> --
> 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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