AMBER Archive (2006)

Subject: Re: AMBER: SHAKE - ntc = 3

From: Jennie Thomas (jenniet_at_uci.edu)
Date: Mon Jan 09 2006 - 19:54:09 CST

This works perfectly! Thanks so much.

Jennie

Bill Ross wrote:

>>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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