AMBER Archive (2009)

Subject: Re: [AMBER] problem with energy calculations

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Jul 12 2009 - 09:15:39 CDT

it's probably easiest to use the imin=5 option in sander (make sure you have
your patches up to date). then you can use your gas phase prmtop from leap
and load the trajectory and calculate energies for each frame without the
extra complication of the mmpbsa scripts. definitely use nobox in ptraj, and
image prior to stripping.

I'm not sure leaving in the counterions in the gas phase makes sense, but
that's more a science issue than technical.

On Sun, Jul 12, 2009 at 10:10 AM, Thomas Lake
<thomas.lake08_at_imperial.ac.uk>wrote:

> My simulations were done in explicit solvent. When I generated the
> prmtop file for the gas-phase peptide, I simply added counterions but no
> solvation. I did not explicitly specify a periodic box, but I dont know
> if LEaP automatically includes it?
>
>
> On Sun, 2009-07-12 at 14:42 +0100, Carlos Simmerling wrote:
> > it's important to make sure that your prmtop and trajectory file match.
> if
> > the prmtop has box info in it (defined in leap) then it needs to be in
> the
> > trajectory as well.
> > it's hard to help at this point because we don't know enough about what
> you
> > did in the simulations. were they in explicit water or in the gas phase?
> how
> > did you set up the original prmtop?
> >
> > On Sun, Jul 12, 2009 at 9:35 AM, Lake, Thomas
> > <thomas.lake08_at_imperial.ac.uk>wrote:
> >
> > > I removed the periodic box from the trajectory file (by specifying
> 'nobox'
> > > in ptraj).
> > >
> > > However I still got this error message.
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > > Behalf Of Carlos Simmerling
> > > Sent: 10 July 2009 18:26
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] problem with energy calculations
> > >
> > > why are you getting virtual box energies in the gas phase? is the
> system
> > > really periodic?
> > >
> > > On Fri, Jul 10, 2009 at 12:13 PM, Thomas Lake
> > > <thomas.lake08_at_imperial.ac.uk>wrote:
> > >
> > > > Hello,
> > > >
> > > > I have been modelling a peptide and am trying to carry out energy
> > > > calculations of it in the gas-phase. For this I use the mm_pbsa
> script,
> > > > but using only MM.
> > > >
> > > > I am able to calculate the energy of just the peptide. However when
> I
> > > > include counterions (but no solvent), I get an error message:
> > > >
> > > > 'The system has extended beyond the extent of virtual box'
> > > >
> > > > If I do reimaging of the trajectory (image center familiar) then I
> dont
> > > > get this error message. However the energies that are calculated
> give
> > > > very high vdW energies for certain frames. This I think is because
> > > > counterions have come into close contact in these frames.
> > > >
> > > > I cannot think of any more possible solutions for this, so wandering
> if
> > > > anyone help me.
> > > >
> > > > Regards
> > > >
> > > > Thomas Lake
> > > > Imperial College London
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
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