Re: AMBER: Group declaration question

From: Bill Ross <>
Date: Wed, 2 May 2007 12:10:23 -0700 (PDT)

> I'm using the Carnal program to calculate the RMS deviation of my side chain
> atoms once the main atoms are fitted. To do this , first I declared, as the
> group 1, the following :
> GROUP grp1 ((RES 200-210, 825-835) & (ATOM NAME C CA N O));
> How can I declare the second group as only the side chains ?
> Is it implemented some kind of boolean operator ?

You should be able to do something like

  GROUP grp2 ((RES 200-210, 825-835) & (!grp1));


  GROUP grp2 ((RES 200-210, 825-835) & !(ATOM NAME C CA N O));

I forget if 'not' is implemented as '!' or NOT.. you will have
to read the manual. Note that carnal isn't supported anymore, so
you may also want to think of switching to ptraj.

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Received on Sun May 06 2007 - 06:07:10 PDT
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