Hi Dong,
You can do selective minimization by use of ibelly.
&cntrl
imin=1,ncyc=500,maxcyc=1000,
ntb=1,ntp=0,ntf=1,ntc=1,
cut=8.0,
ntpr=10,
ibelly=1,
bellymask=':2-300'
/
This will keep residues 2 to 300 fixed during the minimization. So if the
ligand was residue 1 it would then be free to move. You can them obviously
restart this with a more complex mask to allow certain side chains etc to
move. You can also do a flexible type docking/minimization by doing the
above procedure with MD. However, you might want to look into Dock
(
http://dock.compbio.ucsf.edu/) and the option called AMBER dock which
implements the AMBER force field into Dock allowing flexible ligand docking
and minimization.
All the best
Ross
/\
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of Dong Xu
> Sent: Monday, May 12, 2008 3:08 PM
> To: amber.scripps.edu
> Subject: AMBER: Ligand energy minimization
>
> Hi All,
>
> I was wondering about the procedure to set up Amber to perform energy
> minimization of the ligand in the protein binding site environment.
> I'd like to first treat protein rigid and only optimize the ligand. If
> possible, I'd like to also try optimize both ligand and selected
> binding site residues.
>
> Any suggestions are greatly appreciated.
>
> Dong Xu
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Received on Wed May 14 2008 - 06:07:43 PDT
