Hello,
On Fri, Apr 30, 2010 at 1:11 PM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
> Hi Amber users,
>
> I am trying to minimize a protein-ligand complex, solvated with TIP3P water
> (8.0 A).
> I want to restrain atoms that are 8 A beyond some selected binding site
> residues.
> Earlier I used ntr=1 (with force constant 500.0 during minimization and
> 10.0 during MD)
> for restraining protein-ligands during solvent equilibration using group
> list as follows
>
> &cntrl
> ----
> ----
> /
> Hold the protein and ligand
> 500.0
> RES 1-284 (both protein and ligand)
> END
> END
>
> it worked well. Now I am not sure how to mention the distance in these
> inputs.
> For example I want to freeze all atoms(residues & water) that are beyond 8
> A of
> residues 1-3, 4-12. Can someone please tell me how the input should look
> like?
>
I do not know if any defined mask can be dynamically updated during the
course of a simulation (i.e. if a residue moves farther than 8 Å away to
begin restraining it). I think the best you can do is to just choose the
residues outside your cutoff before the simulation starts and define that in
your residue cards at the end of the mdin file or using the "restraintmask"
variable. However, it would seem that if you're only allowing a small
number of residues around the active site to move, the list will probably
not change much during the course of the simulation.
Someone more knowledgeable about the topic may comment further...
Good luck!
Jason
> thanks,
>
> Senthil Natesan
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat May 01 2010 - 16:00:04 PDT
