RE: [AMBER] AMBER11 compilation

From: Steve Seibold <>
Date: Mon, 7 Jun 2010 09:46:03 -0400

Dr. Case
Thanks for your response.

The OS is Linux (running RedHat Enterprise 5)and I did use the gcc compiler (4.1.1). Do the failures mean that umbrella sampling with REMD and the Steered Md application will not function properly?

I did find the *.dif files and the log file containing the "possible failures". The Error seems to be "**NCSU-ERROR** :check list value for key 'i', got '<Empty>' instead". The "possible failures" appear to be differences in numerical outcomes. I attempted to track down this "NCSU-error* and could not find anything substantial.

I have run amber 7 and 8 for several years in parallel. However, a system administrator did all the compiling etc. So, I am a complete novice when it comes to compiling, patching etc..AMBER.

Sorry, I will try to keep my questions to a minimum.

Thanks, Steve

-----Original Message-----
From: [] On Behalf Of case
Sent: Monday, June 07, 2010 8:52 AM
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER11 compilation

On Mon, Jun 07, 2010, Steve Seibold wrote:

> This is my first time compiling AMBER. I followed the instructions
> found in AMBER11 manual and as suggested I first compiled the 'serial'
> version. After running the 'test' it was reported that I had 15
> failures and 1 error shown below: The error was called a "Syntax error".

You should report which OS and compiler you are using. But I'm guessing you have a machine with gcc 4.1.2. This compiler will lead to failures if you use the "abmd" functionality, but should be OK otherwise.

> But, I am not sure if I should move to MPI compilation or not.

You should only proceed to MPI if you know you need parallel capabilities, i.e. if you are planning to run long caclualtions, and have access to parallel computing facilities. New users of Amber should use the serial version to gain familiarity with the program, and only go on to parallel computation when you know it is needed, and you have some understanding of how everything works.


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