AMBER Archive (2006)

Subject: Re: AMBER: SHAKE - ntc = 3

From: David A. Case (
Date: Mon Jan 09 2006 - 16:59:46 CST

On Mon, Jan 09, 2006, Jennie Thomas wrote:

> Thank you for this helpful comment. You are correct, I do not actually
> have O-O bonds defined for each of the nitrate ions. Using rdparm, only
> the three bonds for water and the N-O bonds are listed.
> Looking back at my frcmod file, I can't understand why the O-O bonds are
> not being defined. Any advice on how to force leap to recognize these
> bonds?

The frcmod file just gives parameters; the bonds themselves have to be placed
in whatever residue library file you are using. If you "edit" your residue
in xleap, you can draw in the needed bonds graphically. Or, if you use a mol2
file for the residue, you can add the O-O bonds manually in there. Other
possibilities exist, depending on how you constructed the residue library.

...good luck..dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to