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
> Office: Engineering Building Rm. 2246
>
> Cell: 810-399-6212
>
>
>
>
>
>
>
> _______________________________________________
> 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
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Received on Thu Oct 20 2016 - 12:00:03 PDT
