AMBER Archive (2006)

Subject: Re: AMBER: Sander NOE violations

From: David A. Case (
Date: Thu Jul 06 2006 - 20:41:28 CDT

On Fri, Jul 07, 2006, Andrew Box wrote:

> The restraint file was created by making a 7 column restraint file, then
> converting it with make_dist command.

OK: you will have to examine the output of the make_dist (I assume you mean
makeDIST_RST here) command. That is the file that sander actually reads.
Using the negative pencut option, it should be straightforward to find the
restraints that are giving the funny output, and to debug from there.


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