AMBER Archive (2004)

Subject: Re: AMBER: constraints on atoms

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 21 2004 - 11:12:55 CST

On Mon, Dec 20, 2004, cailliez wrote:

> Group input for protein restraints: 25 kcal/mol.
> 25.0
> RES 1 442
> END
> Atom C from Val 98
> 100.0
> ATOM 1548
> END
> Atom O from Val 98
> 100.0
> ATOM 1549
> END
> END

> Can anyone tell me if this is the right thing to do ?

I don't see anything wrong, offhand. What happens when you run with this
input? The output summarizes what the program is doing.

> And if so, does it mean that for the atoms 1548 and 1549, the constraint
> will be
> (100+25) kcal/mol or just 100 kcal/mol, or even 25 kcal/mol ?

The second constraints should be 100. Again, check the output.

..dac

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