AMBER Archive (2004)

Subject: Re: AMBER: Sander & fix atoms

From: bybaker_at_itsa.ucsf.edu
Date: Thu Jun 03 2004 - 15:54:55 CDT


Hello, Viktor:

Thanks for the help.

I use Amber7 for running sander. The idea is to run energy minimization
on a protein model. The minimization will be done in three steps: (1)
fixed heavy atoms (all but hydrogen), (2) fixed backbone atoms with
tethered atoms, (3) tethered backbone atoms. The structure will be then
subjected to final run with no atom fixed. I am not familiar with
positional restrains. The purpose is to minimize the whole system rather
than the specific fragments.

The follow is my input file. Please fell free to give your comments.

Thank you.

Regards

Bo Yang

------ Start-----
Initial minimization test 1
 &cntrl
     imin=1,
     maxcyc=500,
     ncyc=250,
     ntb=0,
     ntr=0,
  &end
 Group input for restrained heavy atoms (all but hydrogen)
  ATOM ! @H=
  END
 Group input for restrained backbone atoms with tethered atoms
  ATOM @CA, C, O, N
  END
 Group input for tethered backbone atoms
   ATOM @O, H
  END
  END
     
----- End----

On Thu, 03 Jun 2004 13:22:55 -0400 Viktor Hornak wrote:

> bybaker_at_itsa.ucsf.edu wrote:
>
> >Hello, Amber:
> >
> >I would like to run energy minimization in sander with some
> restrictions.
> >
> I'd suggest to use positional restraints (rather than fixing atoms =
> ibelly flag) - check ntr flag in amber manual. You don't say which
> version of amber you are using. Depending on that your input file might
> look differently.
> In amber8, you'd specify 'restraint_wt' and 'restraintmask' in your
> &cntrl input section. This could translate to the following for what you
> want (if I understood your description of restrictions well):
>
> >How can I set the minimization inputs with following restrictions:
> >
> >--- fix heavy (all but hydrogens) atoms
> >
> restraintmask='!@H='
>
> >--- fix backbone atoms
> >
> restraintmask='@CA,C,O,N,H'
>
> >--- fix backbone atoms with tethered heavy atoms
> >
> restraintmask='@CA,C,O,N' (?? - maybe that's not what you want but you
> get an idea)
>
> >--- tethered backbone atoms
> >
> restraintmask='@O,H' (??)
>
> Check chapter 11.5 in amber8 manual for more detailed description of
> selection syntax.
>
> If you are using amber7 or previous, carefully read "GROUP
> specification" appendix in amber manual.
>
> Hope this helps...
>
> -Viktor
>
>
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