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:
JIomm
--- On Sun, 11/29/09, Jack Shultz <js.drugdiscoveryathome.com> wrote:
From: Jack Shultz <js.drugdiscoveryathome.com>
Subject: Re: [AMBER] Scripting tleap
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Sunday, November 29, 2009, 3:54 AM
great I found an example!
On Sat, Nov 28, 2009 at 10:45 PM, Tom Joseph <ttjoseph.gmail.com> 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 <js.drugdiscoveryathome.com>:
>> 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 < tleap.in
>>
>> no luck
>>
>> --
>> Jack
>>
>> http://drugdiscoveryathome.com
>> http://hydrogenathome.org
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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>
--
Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
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Received on Thu Dec 03 2009 - 22:30:03 PST
