Re: [AMBER] AmberTools 1.5 installation problem

From: Siavoush Dastmalchi <Dastmalchi.s.tbzmed.ac.ir>
Date: Thu, 2 Jun 2011 18:51:16 +0330

Thanks for the replies,
 
In fact I am using an old version of Fedora. It is ver 5 FC.
here are the versions of ifort and other compilers:
 
[amber11.Cluster-Node-1 ~]$ more /etc/fedora-release
Fedora Core release 5 (Bordeaux)
[amber11.Cluster-Node-1 ~]$ ifort --version
ifort (IFORT) 10.1 20070913
Copyright (C) 1985-2007 Intel Corporation. All rights reserved.
[amber11.Cluster-Node-1 ~]$ cc --version
cc (GCC) 4.1.0 20060304 (Red Hat 4.1.0-3)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[amber11.Cluster-Node-1 ~]$ gcc --version
gcc (GCC) 4.1.0 20060304 (Red Hat 4.1.0-3)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I haven't tried to see exactly what is working what is not. For example, I am able to use tleap tools, but I can see that, for instance, MMPBSA.py is not in the specified place. In fact I use Amber9, but for doing some residue-based analyses on mmpbsa results, I realized that I need to use python version of it. So I decided to install AmberTools 1.5.
I am not sure, but could that be because I haven't installed Amber11?
 
Cheers,
Siavoush

________________________________

From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: Thu 6/2/2011 4:46 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AmberTools 1.5 installation problem



On Thu, Jun 02, 2011, Siavoush Dastmalchi wrote:
>
> I was trying to install AmberTools 1.5, but have faced
> with couple of problem. I have downloaded it from
> http://ambermd.org/AmberTools-get.html and then copied the bugfix.all
> patch to $AMBERHOME directory. Then I did all the steps as instructed
> in the manual. First time I used gnu compilers but it failed, then I
> used intel compilers. It didn't finish without error but was much much
> better. When I performed the test, in majority of the cases the test
> passed and at the end I got the following lines showing that there are
> some problems.

Your results look fine to me. The "errors" in the summary are listed because
the script reports an "error" if Amber11 is not installed, but that is the
wrong word to be using. [Any developer want to try to make the output better
if Amber11 is not installed?]

We'd really like to know what problems you had with the gnu compilers,
since we use them all the time, and they are generally compatible with
AmberTools. Which version did you use ("gcc --version"), which OS, and
what was the problem?

...thanks...dac


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Received on Thu Jun 02 2011 - 07:30:03 PDT
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