AMBER Archive (2009)

Subject: [AMBER] error in xleap: ligand binding using MMand QMMM tech

From: kureeckal ramesh (kureeckalramesh_at_yahoo.co.in)
Date: Thu Feb 12 2009 - 04:27:41 CST

Hi Amber Users,

I am working on "Ligand Binding using MM and QMMM techniques" using AMBER10 package.
1) Though AMBER9 is recommended (www.rosswalker.co.uk/tutorials/psc_workshop/htm), I am able to execute first few commands of the above tutorial using AMBER10 (i,e precisley upto "using Leap for protein, ligand separately).
2) While "using leap for building the complex", I am able to execute only a part of the commands (explained below):
=============================================
xleap is able to execute :
source leaprc.ff03
source leaprc.gaff
mods=loadamberparams TAZ.frcmod
==============================================

3) while I execute the command :
TAZ=loadmol2 TAZ.mol2
following error is got , which is pasted at the bottom:
===================================================================
../xleap: line 11:  4470 Segmentation fault      /usr/local/amber10/amber10/exe/xaLeap -I/usr/local/amber10/amber10/dat/leap/prep -I/usr/local/amber10/amber10/dat/leap/lib -I/usr/local/amber10/amber10/dat/leap/parm -I/usr/local/amber10/amber10/dat/leap/cmd $*
===================================================================

Can I use AMBER10 package for the above tutorial. Am I going wrong while calling xleap command. I request any one of you to help me out in solving this error. Looking forward for your valuable suggestions

With regards
Ramesh K V

--- On Mon, 2/2/09, kureeckal ramesh <kureeckalramesh_at_yahoo.co.in> wrote:
From: kureeckal ramesh <kureeckalramesh_at_yahoo.co.in>
Subject: Re: [AMBER] Dr. Ramesh here
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Monday, 2 February, 2009, 7:52 PM

Hello Sir,
Thanks for your reply. I shall attend to the corrections

With regards
Ramesh K V

--- On Fri, 30/1/09, David A. Case <case_at_biomaps.rutgers.edu> wrote:
From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: [AMBER] Dr. Ramesh here
To: kureeckalramesh_at_yahoo.co.in, "AMBER Mailing List" <amber_at_ambermd.org>
Date: Friday, 30 January, 2009, 9:38 PM

On Fri, Jan 30, 2009, kureeckal ramesh wrote:

> Running: /usr/local/amber10/amber10/bin/mopac.sh
> /usr/local/amber10/amber10/bin/mopac.sh: line 12:
/usr/local/amber10/amber10/bin/mopac: is a directory

This is weird: the "mopac" in the bin directory should be an
executable
file, not a directory. Can you
 check what is going on there? Perhaps
you should remove the existing /usr/local/amber10/amber10/bin/mopac, and
recompile antechamber...

....dac

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