AMBER Archive (2007)

Subject: Re: AMBER: command tleap is not normal

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Aug 21 2007 - 03:50:35 CDT

Dear Qiang,

There is nothing wrong with what you are experiencing. In tleap (or
xleap), you can write 'help' to see what kind of commands you can use in
Leap. For instance, if you want to call a particular force field, you need
to use the command 'source <name of the force field>'. The force field can
be 'leaprc.ff99', 'leaprc.rna.ff99', etc. It is better for you to follow
the first tutorial in the AMBER website, as I can see that you are new to
AMBER package. Following the other tutorials will help you to understand
the logic on how AMBER is working.

Good luck,

On Tue, 21 Aug 2007, Qiang Zhong wrote:

> Dear Amber users:
> I am preparing top file of protein simulation.when I execute tleap
> command, I get
> below information ,it is not like tutorial .
> [t_at_localhost ~]$ tleap
> -I: Adding /home/internet/Soft/Amber/amber9/dat/leap/prep to search path.
> -I: Adding /home/internet/Soft/Amber/amber9/dat/leap/lib to search path.
> -I: Adding /home/internet/Soft/Amber/amber9/dat/leap/parm to search path.
> -I: Adding /home/internet/Soft/Amber/amber9/dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
> >
>
> in tutorial file, normal result should be:
>
> 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
> >
>
> Could somebody tell me what the problem with it,and what shall I do?
> Thank you very much!
>
>
>
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemistry      -				-
  - University of Rochester      -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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