Re: [AMBER] Fwd: neighbours around an atom

From: Jason Swails <>
Date: Sat, 5 Jul 2014 07:31:39 -0700

On Sat, Jul 5, 2014 at 7:18 AM, Krisztina Fehér <>

> Thanks for the shell script, Dan.
> One more question: can you combine a distance-based criterion with an
> atom name selection? So, is it possible to select e.g. carbonyl atoms
> within 5A distance from :4.SG? I tried to join these two selections
> with "&":
> .C&:4.SG<:5.0

​This is probably interpreted as (@C&:4.SG) < :5.0, which would not match

> and
> :4.SG<:5.0&.C
> which did not work and would like to know why. Is there a limitation
> in the use of the logical operators?

​Maybe try parentheses:

(:4.SG<:5.0)&.C or .C&(:4.SG<:5.0)

You can increase the print level of mask evaluation (using the "prnlev"
command, I think). This should show you the prefix and postfix notation
that will more clearly represent how the mask is actually being evaluated
if you continue to have troubles with masks.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat Jul 05 2014 - 08:00:03 PDT
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