Thanks!
That's working now, but of course the next stage is not:
> solvateBox mol WATBOX216 10
solvateBox: Argument #2 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
Would you be so kind to tell me what is wrong now?
> solvateBox mol WATBOX216 10
Is copied from the tutorial.....
Thanks!!
Fabian
_______________________________
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
On Nov 4, 2012, at 5:14 PM, Jason Swails wrote:
>
>
> On Nov 4, 2012, at 9:37 AM, Fabian Glaser <fglaser.technion.ac.il> wrote:
>
>> Dear all,
>>
>> I have recently purchased amber, so forgive me if my questions are a little trivial.
>>
>> I am trying to follow tutorial A8, which starts by uploading tleap program and paths (I am using a mac OSX sytem), the problem is that despite that (I think) I updated correctly the AMBEHOME PATH in my .bash_profile, in which I added the lines:
>>
>> export AMBERHOME=/Users/fabian/TOOLS/amber/amber12
>> export AMBERTOOLS=$AMBERHOME/AmberTools/bin
>> export FPOCKET=/Users/fabian/TOOLS/fpocket/fpocket2/bin
>>
>> PATH=${PATH}:${PDB_TOOLS}:${IUPred_PATH}:${PDB_CENTRALITY}:${AMBERHOME}:${AMBERTOOLS}:${AMBERHOME}/bin
>
> I would only add AMBERHOME/bin to PATH, not AMBERHOME by itself. And none of the AMBERTOOLS variables are necessary (the AmberTools bin directory is just a link to the Amber bin directory).
>
>>
>> The tleap program starts with a path problem:
>>
>> fabian.fabians-imac { ..A8 }-> tleap
>> -I: Adding /Users/fabian/TOOLS/amber/amber12/dat/leap/prep to search path.
>> -I: Adding /Users/fabian/TOOLS/amber/amber12/dat/leap/lib to search path.
>> -I: Adding /Users/fabian/TOOLS/amber/amber12/dat/leap/parm to search path.
>> -I: Adding /Users/fabian/TOOLS/amber/amber12/dat/leap/cmd to search path.
>>
>> Welcome to LEaP!
>> (no leaprc in search path)
>
> This is normal. If you want to set up a default force field that you ALWAYS want to use, then copy the leaprc for that force field (e.g., leaprc.ff12SB) to the file name leaprc in AMBERHOME/dat/leap/cmd. Or you can copy the leaprc that you want for a specific project in your current working directory.
>
> What I usually do, though, is just write a tleap script in which I source the leaprc I want (leaprc.ff12SB) at the top of the script and load all of the other files I need separately.
>
> Hopefully this will make more sense as you work through the tutorial.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sun Nov 04 2012 - 07:30:03 PST
