AMBER Archive (2005)

Subject: Re: AMBER: Protein with structural ions

From: David A. Case (case_at_scripps.edu)
Date: Sun Apr 10 2005 - 23:04:52 CDT

On Sun, Apr 10, 2005, Kara Di Giorgio wrote:

> I've created a .refc file with my four distance restraints in it. I
> think I have the correct format. I have figured out I need to add -ref
> to the sander command line when I start my simulation.

The -ref flags refers to "reference coordinates" used with the ntr=1 option.
It would not have anything to do with distance constraints.

>
> Right now, I'm not sure how to include the fact that I have distance
> restraints in the md.in file. I've tried nmropt =1, nmropt =2 and
> nmropt >1 and none of them work. What is the correct flag to use?

You give the file name containing distance retraints in a DISANG=<filename>
line in the input file, and set nmropt=1.

...dac

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