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.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.ambermd.org [mailto:amber-bounces.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.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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Received on Sun Jul 12 2009 - 10:09:23 PDT
