Thankyou very much for that.
I've compiled AT12 with all the bugfixes and cpptraj works like a treat, excellent!
Kind regards,
Andre
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Friday, 4 May 2012 8:39 PM
To: AMBER Mailing List
Subject: Re: [AMBER] ptraj closest water script problem
Hi,
On Fri, May 4, 2012 at 5:39 AM, Thomas Cheatham <tec3.utah.edu> wrote:
> The key is how you view with VMD. You cannot load the original prmtop
> file since this will have all the waters; there is no information in
> the trajectory file to specify what atom is what, only a list of x, y,
> z for atoms 1->N. Therefore you need some way to map and this requires
> either loading a corresponding PDB file (with no ions and only 10
> waters) or a corresponding prmtop file (with no ions and only 10 waters).
Note that AT12 cpptraj can now generate a matching prmtop for you automatically:
trajin md_reimaged.mdcrd 201 400
trajout closest_waters.mdcrd
strip :Na+
closest 10 :13 oxygen outprefix strip
This will create a prmtop that matches the output from 'closest'
called strip.<parmname> where <parmname> is your original parm filename. If you use cpptraj though make sure the latest bugfixes are applied since AT12 bugfix 5 applies to cpptraj 'closest'.
-Dan
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Received on Sun May 06 2012 - 21:00:03 PDT
