AMBER Archive (2009)

Subject: [AMBER] error in tleap of AMBER 10

From: kureeckal ramesh (kureeckalramesh_at_yahoo.co.in)
Date: Fri Jun 26 2009 - 02:10:56 CDT

Dear Dave
Thank you for your reply. I did try running the tleap command but the job crashed.
As per your suggestion I am pasting the information of TAZ.mol2 file and also the information about the OS and compiler

1) Information about the OS and the compiler
CentOS release 5.2
gcc (GCC) 4.1.2 20071124

2) TAZ..mol2 file is sent as an attachment

With regards
Ramesh K V

--------------------------------------------------------------------------

--- On Thu, 25/6/09, case <case_at_biomaps.rutgers.edu> wrote:

From: case <case_at_biomaps.rutgers.edu>
Subject: Re: [AMBER] error in tleap of AMBER 10
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Thursday, 25 June, 2009, 5:24 PM

On Wed, Jun 24, 2009, kureeckal ramesh wrote:

> (1) I am working with the AMBER tutorials titled " Ligand
> Binding using MM and QMMM techniques." available at
> http://www.rosswalker.co.uk/tutorials/psc_workshop/contents.htm.Â

Well, this is old...

> Loading Mol2 file: ./TAZ.mol2
> Reading MOLECULE named TAZ
> ../tleap: line 9: 8766 Segmentation fault    Â
> /usr/local/amber10/bin/teLeap -I/usr/local/amber10/dat/leap/prep
> -I/usr/local/amber10/dat/leap/lib -I/usr/local/amber10/dat/leap/parm
> -I/usr/local/amber10/dat/leap/cmd $*

As I see it, this tutorial requires you to create your own TAZ.mol2 file, and
it seems likely that something went wrong at that step.  (The tutorial works
fine for me in Amber10.)

So, take a look at your TAZ.mol2 file, and see if everything looks OK.  If you
can't figure out the problem, make sure that a very simple tleap run (just
with "taz = loadmol2 TAZ.mol2") job still crashes, and post the mol2 file,
along with info about your OS and compiler.

....dac

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  • application/octet-stream attachment: TAZ.mol2

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