Re: [AMBER] cpptraj and selection

From: Daniel Roe <>
Date: Thu, 13 Oct 2016 08:50:40 -0400


It would be best if you gave a description of what you're trying to
select, but I will give what comments I can on the selections you have
tried. FYI section 29.2.2 'Atom Mask Selection Syntax' in the Amber 16
manual is a pretty good primer on Amber style mask expressions.

On Sun, Oct 9, 2016 at 9:56 PM, Dhiraj Srivastava <> wrote:
> Hi All
> for the allignment and rmsd calculation, I am trying to use only a
> range of residues and not the entire structure because of flexibility of
> one domain. but the flexible domain is in the middle of structure. I tried
> saveral diferent possibility but none of them appeared to work. like
> .CA!:110-220

This mask is not valid and I think should kick back an error.

> .CA&!:110-220

This mask should work I think; it should select all CA atoms not in
residues 110 to 220.

> :14-109.CA,221-531.CA

This is also an invalid mask and will probably give you weird behavior.

> :14-109,221-531.CA

This is the correct way to specify the previous mask and will give you
CA atoms from residues 14-109 and 221-531.

> and so on. but none of them is giving me correct number of residues used in
> alignment. what's the best way to do this?

If you can provide a better description of your system and what you
want to select we may be able to help further.


> Thanks
> Dhiraj
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Thu Oct 13 2016 - 06:00:05 PDT
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