AMBER Archive (2008)

Subject: RE: AMBER: Clarification on error message

From: Campbell, Patrick (
Date: Sat Mar 08 2008 - 15:15:36 CST

Thanks for the quick response Dr. Steinbrecher. It would appear that the error lay in the absence of the -ref switch in the sander command - the ntr parameter was set correctly. I have since made the necessary adjustment and have resubmitted my job for processing.

Thanks again and do have a great day!

-----Original Message-----
From: [] On Behalf Of Thomas Steinbrecher
Sent: Saturday, March 08, 2008 2:18 PM
Subject: Re: AMBER: Clarification on error message

Hi Patrick,

did you specify a reference coordinate file with the -ref switch in your
sander command? If yes, is that file present and readable to your process?
Did you set ntr=1 in your mdin file so that sander expects a reference



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Sat, 8 Mar 2008, Campbell, Patrick wrote:

> Good Morning AMBER Analysts,
> I have an error in a minimization output file which I was hoping you would clarify.
> Unit   10 Error on OPEN: refc
> I have attached the output file for reference.
> Thanks for your assistance and do have a great day!
> Patrick
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