AMBER Archive (2008)

Subject: RE: AMBER: Ligand energy minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 13 2008 - 10:14:53 CDT

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

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Dong Xu
> Sent: Monday, May 12, 2008 3:08 PM
> To: amber_at_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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu