AMBER Archive (2006)

Subject: Re: AMBER: Problem with mask when using distance in ptraj

From: Thomas Cheatham (
Date: Wed Nov 22 2006 - 15:17:12 CST

> > Mask [@CA:244] represents 0 atoms !!!NO ATOMS DETECTED!!!
> You can use the ambmask command to play around with various masks to get
> what you want. Have you tried ':544_at_CA'? All the examples in the Users'
> Manual have the residue specification to the left of the atom specification,
> and maybe that is required(?).

Yes, residue specification must be first. Also, there is a "checkmask"
command in the "rdparm" version of ptraj.

  rdparm prmtop
  checkmask :244_at_CA

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