Re: [AMBER] Scripting tleap

From: Jio M <>
Date: Thu, 3 Dec 2009 22:04:01 -0800 (PST)

Dear Amber users;

I have some problem in using -f flag with tleap.

I want to use set command(s) which are in .txt file. tleap "source" the text file but donot go beyond loading abc.lib


my.txt file contains this:

loadoff abc.lib

set b head b.1.N1

set c head c.1.N1


And I am using following:

tleap -f /opt/amber10/dat/leap/cmd/leaprc.gaff -f my.txt

-I: Adding /opt/amber10/dat/leap/prep to search path.

-I: Adding /opt/amber10/dat/leap/lib to search path.

-I: Adding /opt/amber10/dat/leap/parm to search path.

-I: Adding /opt/amber10/dat/leap/cmd to search path.

-f: Source /opt/amber10/dat/leap/cmd/leaprc.gaff.

-f: Source my.txt.

Welcome to LEaP!

(no leaprc in search path)

Sourcing: /opt/amber10/dat/leap/cmd/leaprc.gaff

Log file: ./leap.log

Loading parameters: /opt/amber10/dat/leap/parm/gaff.dat

Reading title:

AMBER General Force Field for organic mol., add. info. at the end (June, 2003)

Sourcing: ./my.txt

Loading library: ./abc.lib

Beyond this leap does not read the set command in my.txt file. I have tried in different ways also but its not working

Please suggest anything I am missing here.

thanks and regards:


--- On Sun, 11/29/09, Jack Shultz <> wrote:

From: Jack Shultz <>
Subject: Re: [AMBER] Scripting tleap
To: "AMBER Mailing List" <>
Date: Sunday, November 29, 2009, 3:54 AM

great I found an example!

On Sat, Nov 28, 2009 at 10:45 PM, Tom Joseph <> wrote:
> Put your commands in a separate file and use the -f flag to tleap, as
> you did for leaprc.ff99SB.
> --Tom
> 2009/11/28 Jack Shultz <>:
>> I am trying to send some arguments to tleap. Is there a way to pass
>> these through a script.
>> str1=loadpdb pdb100d.ent
>> savepdb str1 pdb100d.pdb
>> quit
>> I tried writing a file then redirecting input to it
>> tleap -f /usr/local/antechamber-1.27/dat/leap/cmd/leaprc.ff99SB <
>> no luck
>> --
>> Jack
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

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Received on Thu Dec 03 2009 - 22:30:03 PST
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