Re: AMBER: Once again, "distance" command in ptraj

From: Roberto Veiga <>
Date: Tue, 5 Jun 2007 11:20:27 +0200

Dear Prof. Cheatham:

a fragment of the output follows.


FYI: No output trajectory specified (trajout), none will be saved.

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 1000 frames.
       Summary of I/O and actions follows:

  File (../prod.mdcrd) is an AMBER trajectory (with box info) with 1000 sets

  NULL entry

  1> CENTER to origin via center of geometry, atom selection follows :391
  7> IMAGE by molecule to origin using the center of mass, atom
selection * (All atoms are selected)
  7> DISTANCE: between the atoms selections center of mass will be
      saved to array named efesf
      Atom selection 1 is :391.Na+
      Atom selection 2 is :60.CZ
      Data will be dumped to a file named dist

Processing AMBER trajectory file ../prod.mdcrd
  DISTANCE: box angles are zero, disabling imaging!




2007/6/5, Thomas Cheatham <>:
> > trajin ../prod.mdcrd
> > center :391 origin
> > image origin center
> > strip :WAT,OCT
> > distance dist :60,157,254,351.CZ,CG,CD*,CE* :391 dist.list
> I'm traveling so have sporatic e-mail, but my guess is that the "strip"
> command is somehow invalidating the box information. Try moving the strip
> to after the distance measurement... In the meantime, I'll track it down.
> Also, Prof. Simmerling is partially correct; by default, if box
> information is present, the distance command calculates the minimum imaged
> distance regardless of your center/image specifications (unless you
> specify the "noimage" keyword). The intent is/was to show the shortest
> distance in periodic space. I think that somehow the "strip" is disabling
> this, assuming you are correct that the trajectory has box information and
> the prmtop had it and/or you specified it with the "box"
> command..... likely it is a bug or feature, but I agree that the strip
> should not automagically lead to ignoring the box info.
> [If I do not respond back soon; e-mail me privately and I'll try to
> decipher].
> -- tec3
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Received on Wed Jun 06 2007 - 06:07:29 PDT
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