AMBER Archive (2009)

Subject: Re: [AMBER] Scripting tleap

From: Jio M (jiomm_at_yahoo.com)
Date: Fri Dec 04 2009 - 00:04:01 CST

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_at_drugdiscoveryathome.com> wrote:

From: Jack Shultz <js_at_drugdiscoveryathome.com>
Subject: Re: [AMBER] Scripting tleap
To: "AMBER Mailing List" <amber_at_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_at_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_at_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
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber