AMBER Archive (2006)

Subject: Re: AMBER: NMR restraints and LES

From: David A. Case (case_at_scripps.edu)
Date: Mon Feb 20 2006 - 20:26:17 CST

On Mon, Feb 20, 2006, Sivakolundu, Sivashankar wrote:

> I have a question about using NMR restraints in conjunction with LES.
> The Amber manual says that the NMR restraints are "ensemble averaged"
> when it is used with LES option. I would like to know how the NMR
> restraints are applied on the LES copies. Say for example I have an NMR
> restraint of 4A between atoms A and B (d(AB)) and I make three LES
> copies, then is the restraint applied like this:
>
> d1(AB)=4; d2(AB)=4; d3(AB)=4;
>
> or like this
>
> (d1(AB)+d2(AB)+d3(AB))/3 =4;
>

It is much more like the latter than the former, but there are details that
depend on the type of averaging, and on whether atoms A and B are in the same
LES group, or in different groups.

The thing to do is to study carefully the output file created by makeDIST_RST
when the "-les" flag is turned on. This will show you exactly what
constraints are being computed. Start with some simple constraint lists (e.g.
just a single constraint, as above), and see what you get. Sander is very
"dumb" in this respect: it just computes whatever is in the restraint file.
So, if you can grok the input, you shold know what is going on.

...good luck...dac
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