Re: [AMBER] Using restraints to get a complex

From: David A Case <>
Date: Thu, 8 Jan 2015 22:06:35 -0500

On Thu, Jan 08, 2015, wrote:

> Reading on the mailing list, I thought that EMAP restraints based on
> the starting coordinates for each of the domains might keep the domains
> compact. When I tried that, I didn't see any difference with the EMAP
> free simulation.

Can you be more specific about exactly what "didn't see any difference" means?
You should certainly see information in the output file describing the emap
constraints, and there should be lines beginning with " EMAP" for every step
that is printed out. Is the EMAP (pseduo-)energy changing with time?

Take a look at the examples in $AMBERHOME/test/emap and $AMBERHOME/test/emap2.
Compare what you are doing to what is done there.

Your value for fcons looks to be 2 to 3 orders of magnitude too large.
But that should lead to problems with the simulation, not with "no


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Received on Thu Jan 08 2015 - 19:30:02 PST
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