Re: [AMBER] ambmask and periodic boundaries

From: Aseel Bala <balaahme.msu.edu> Date: Thu, 20 Oct 2016 15:53:02 -0400

--
Aseel Bala Ahmed
PhD Candidate, Chemical Engineering
Michigan State University
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com] 
Sent: Thursday, October 20, 2016 2:45 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] ambmask and periodic boundaries
Hi,
I recommend centering and imaging around your residue of interest in
cpptraj, then use the 'mask' command to print a pdb file via the following
input:
parm simbox.prmtop
trajin frame3302.inpcrd
center :3 origin
image origin center familiar
mask :3 <:3.0 maskpdb output.pdb
You could also try substituting 'autoimage' for the 'center'/'image'
commands.
Hope this helps,
-Dan
On Thu, Oct 20, 2016 at 2:41 PM, Aseel Bala <balaahme.msu.edu> wrote:
> Hi all,
>
>
>
> I am currently trying to use ambmask to identify all the molecules 
> within a certain distance (3 Angstroms) of a given molecule.
>
>
>
> I have been using ambmask as follows:
>
> ambmask -p simbox.prmtop -c frame3302.inpcrd -find ':3 <:3.0' > 
> output.pdb
>
>
>
> My problem is: when I ran the MD simulation to obtain the coordinates 
> in frame3302.inpcrd, I had periodic boundaries activated (constant
pressure).
>
> However when ambmask runs, it doesn't pick up images across a periodic 
> boundary that are within the distance I chose (in this case 3 
> angstrom. It is only picking up the molecules within the original box 
> that are within that range.
>
>
>
> Is there a way to get amber to find all molecules (original and image) 
> that are within 3 angstroms of the molecule I am interested in?
>
>
>
> Any help will be very much appreciated!
>
>
>
> Thanks,
>
> --
>
>
>
> Aseel Bala Ahmed
>
> PhD Candidate, Chemical Engineering
>
> Michigan State University
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber