AMBER Archive (2006)

Subject: Re: AMBER: minimization with my own charges

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Aug 31 2006 - 17:50:26 CDT

I assume that you did not create any residue library, which has your new
charges in it. You have to do this first. The easiest way is to do this in
xleap. In xleap, load the standard force field file. When u write 'list',
you will see the residues that are defined. You can edit any of these
residues and change the charges. Then, use the saveoff command in xleap to
create the residue library file for this residue (.off file). Do the same
thing for all of the residues which have different charge distribution. U
can load these .off library files later. When u load them in xleap, u will
see that the residues have your new charge information in them.

I would strongly suggest you to do the DNA and Thermodynamic Integration
tutorials to get familiar with creating new residue library files and
doing minimizations using sander. Good luck.

Best,

On Thu, 31 Aug 2006, Myunggi Yi wrote:

> My resdiues are nomal amino acids.
> Their charges charges are slightl different from the orignal one.
> I'm looking for the simplest way.
>
>
> On 8/31/06, Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
> > Dear Myunggi,
> >
> > Do u have the new residue library, which includes your charges? If yes, u
> > should create the prmtop and inpcrd files in xleap using this library for
> > your structure. U will use the normal sander program of AMBER 9 if u want
> > to minimize the structure. If u are not using the Thermodynamic
> > Integration Approach, sander is not different (just for the records, if u
> > want to do TI calculation, u need to use sander.MPI in AMBER 9, which is
> > running sander in parallel mode). Good luck.
> >
> > Best,
> >
> > On Thu, 31 Aug 2006, Myunggi Yi wrote:
> >
> > > Dear Amber users,
> > >
> > > I want to minimize a structure with my own charges for some residues.
> > > I think a simple way to assign my charges is using free energy perturbation.
> > >
> > > I don't want the free energy calculation.
> > > I will do only minimization with the perturbed charges.
> > >
> > > It seems amber 9 is different from amber 7.
> > >
> > > Would you suggest some idea?
> > >
> > >
> > >
> >
> > --
> > Ilyas Yildirim
> > ---------------------------------------------------------------
> > - Department of Chemisty - -
> > - University of Rochester - -
> > - Hutchison Hall, # B10 - -
> > - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> > - http://www.pas.rochester.edu/~yildirim/ -
> > ---------------------------------------------------------------
> >
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>
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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