AMBER Archive (2006)

Subject: Re: AMBER: SHAKE - ntc = 3

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Mon Jan 09 2006 - 18:07:47 CST

I have an no3.lib file that was provided by one of my collaborators:
https://webfiles.uci.edu/jenniet/no3/no3.lib

However there must be a problem with it, since the O-O bonds are not
defined in the rdparm file. Is there a quick way to check where the
error is in this .lib file? Or, is there an easy way to regenerate this
file?

I'm a bit new working with Amber force fields, so your help is appreciated!

With thanks,
Jennie Thomas

David A. Case wrote:

>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
>
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