Re: [AMBER] Sander error (AmberTools 13 & Amber10)

From: Concha, Monica <Monica.Concha.ARS.USDA.GOV>
Date: Thu, 31 Oct 2013 21:40:54 +0000

Daniel Roe,
Thanks for your help!
there is only one machine, the cluster.

I got new error when I add that directory to my LD_LIBRARY_PATH variable.
$AMBERHOME/bin/sander -O -i -o polyAT_vac.out -c polyAT_vac.inpcrd -p polyAT_vac.prmtop -r polyAT_vac.rst
/home/glenn/amber10_distribution/amber10/bin/sander: error while loading shared libraries: cannot open shared object file: No such file or directory

I just found the code (Amber10.tar.bz2, AmberTools-1.2.tar.bz2) so I'll recompile them.

Any tips before I recompile Amber10 will be greatly appreciated!

Monica C. Concha
Physical Science Technician
Cotton Structure and Quality Research
Southern Regional Research Center
1100 Robert E. Lee Blvd.
New Orleans, LA 70124
phone: 504-286-4252

-----Original Message-----
From: Daniel Roe []
Sent: Thursday, October 31, 2013 2:24 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Sander error (AmberTools 13 & Amber10)


On Thu, Oct 31, 2013 at 10:51 AM, Concha, Monica <> wrote:
> Amber10 was installed for somebody else and he's not working here anymore.

Was it installed on a cluster or on the machine you are working on?
Your best bet is probably to recompile the code. If that's not an option, you can try to find the right (using locate and add that directory to your LD_LIBRARY_PATH variable. However, if you've got multiple versions of GNU compilers installed on the machine that could be problematic.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Oct 31 2013 - 15:00:02 PDT
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