AMBER Archive (2002)

Subject: Re: Recalculating energies

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Wed Apr 17 2002 - 06:39:27 CDT

In AMBER6 sander (not sander_classic) you can read the mdcrd
file and calculate energies . Make sure to use a copy of the
mdcrd file in case something goes wrong. You may have to
recompile sander with the -DTRAJ_ENE in the MACHINE file
if it wasn't already done that way. In AMBER7 it is on by default.
Make sure to set imin=5. This will carry out a minimization for
each frame of the trajectory. Set maxcyc=1 if you don't want to keep
minimizing, you can even set dx0 very small if you are concerned
about one step of minimization.
Carlos
=====================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Department of Chemistry Fax: (631) 632-1555
SUNY at Stony Brook Web:
<http://comp.chem.stonybrook.edu/carlos>
Stony Brook, NY 11794-3400 E-mail:
carlos.simmerling_at_stonybrook.edu
=====================================================

----- Original Message -----
From: "John Finke" <jfinke_at_chem.ucsd.edu>
To: "Carlos Simmerling" <carlos.simmerling_at_sunysb.edu>
Cc: "John Finke" <jfinke_at_chem.ucsd.edu>
Sent: Wednesday, April 17, 2002 1:02 AM
Subject: Re: Recalculating energies

>
> The parm.top was created using AMBER4.1 and the mdcrd was obtained using
> sander_classic of AMBER version 6.
>
> Currently, I have a file "mden", which lists the energy of each
> configuration from the mdcrd output. I would like to be able to use
> whatever AMBER tools available to create a new "mden" file using a
> new modified parm.top but using the old mdcrd.
>
> Thanks for your help.
>
> John Finke
> jfinke_at_ucsd.edu
>
>
> On Tue, 16 Apr 2002, Carlos Simmerling wrote:
>
> > John,
> > this can be done, how depends on amber version.
> > let me know what you're using and I can let you know if/how.
> > Carlos
> > =====================================================
> > Carlos L. Simmerling, Ph.D.
> > Assistant Professor Phone: (631)
632-1336
> > Department of Chemistry Fax: (631) 632-1555
> > SUNY at Stony Brook Web:
> > <http://comp.chem.stonybrook.edu/carlos>
> > Stony Brook, NY 11794-3400 E-mail:
> > carlos.simmerling_at_stonybrook.edu
> > =====================================================
> >
> > ----- Original Message -----
> > From: "John Finke" <jfinke_at_chem.ucsd.edu>
> > To: <amber_at_heimdal.compchem.ucsf.edu>
> > Sent: Tuesday, April 16, 2002 8:45 PM
> > Subject: Recalculating energies
> >
> >
> > >
> > > Is there an easy way to re-calculate energies for configurations from
an
> > > md simulation using a new "mutated" parm.top (i.e. Free Energy
> > > Perturbation)?
> > >
> > > I tried looking into carnal to compute the new energy values for each
> > > iteration but it only appears to compute mostly structural properties
of
> > > the configurations.
> > >
> > > John Finke
> > > jfinke_at_ucsd.edu
> > >
> > >
> > >
> > >
> > >
> > >
> >
> >
>