Re: [AMBER] use of "ambmask" ? & freezing selected residues

From: Senthil Natesan <sen.natesan.yahoo.com>
Date: Tue, 4 May 2010 14:23:32 -0700 (PDT)

Hi Ben,

Thank you so much for the reply. Now I figured out how to specify residues or atoms
to be restrained. I wanted to freeze all atoms that are 8 A beyond the binding site residues.
so my input file has the following lines and it run successfully.

&cntrl 
----
----
---
ntr =1,
restraint_wt=200.0,
restraintmask=':23,46,91-95,144-146,159-160 >.8.0'
/
The .out file has the following lines to verify my selection
---------------------------------------------------------------------
LOADING THE CONSTRAINED ATOMS AS GROUPS
    5. REFERENCE ATOM COORDINATES
    traj
        Mask :23,46,91-95,144-146,159-160 >.8.0; matches 26217 atoms
Thanks again,
Senthil Natesan
Hi Senthil,
On 3/5/2010, at 11:52 a.m., Senthil Natesan wrote:
> Can anyone please point me out the applications (with simple examples)
> of the command "AMBMASK" ? I understand that it helps in filtering selected residue/atoms.
> Can it be used to create input files specifying residues/atoms that should be restrained 
> during MD/minimization?
ambmask doesn't so much generate files as identify which atoms, if any, will be identified by a particular mask. Once you've established what mask you want, you can supply it as a string, enclosed within 'single quotation marks', to e.g. restraintmask in your mdin file.
For more information on how masks are constructed and how ambmask is to be used, you're invited to look at page 267 and following pages in the Amber 11 manual (or its equivalent in earlier versions of the manual).
Hope that helps.
Ben
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Received on Tue May 04 2010 - 14:30:05 PDT
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