AMBER Archive (2006)

Subject: Re: AMBER: SHAKE - ntc = 3

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jan 09 2006 - 18:39:12 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?

Here we see the atoms:

 "OO1" "ON" 0 1 196611 1 8 -0.650000
 "NN1" "NO" 0 1 196611 2 7 0.950000
 "OO2" "ON" 0 1 196611 3 8 -0.650000
 "OO3" "ON" 0 1 196611 4 8 -0.650000

And here are the bonds:

!entry.NO3.unit.connectivity table int atom1x int atom2x int flags
 1 2 1
 2 3 1
 2 4 1

"int atom1x int atom2x int flags" tells us the numbers are atom, atom, flag.
So 1 is connected to 2, and 2 is also connected to 3 and 4.

Quite likely you could bond the O's by adding these lines to the
bond list:

 1 3 1
 1 4 1
 3 4 1

Bill
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