AMBER Archive (2005)

Subject: Re: AMBER: mm/pbsa error

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Wed Jun 01 2005 - 12:23:53 CDT

What if I do not want to include water from previous md simulations?

On 5/10/05, Scott Pendley <scott.pendley_at_gmail.com> wrote:
> I ran into a similiar problem when I was using ptraj to strip water,
> ions from my trajectories prior to importing them into mm_pbsa. I
> found that in these cases, if I left the water and ions in and
> adjusted the parameters for total atoms to compensate, the mm_pbsa
> energetics calculations went smoothly.
>
> On 5/4/05, Eric Hu <eric.y.hu_at_gmail.com> wrote:
> > Hi I ran into an error when doing nm calculation.
> >
> > @GENERAL
> > PREFIX pepB
> > PATH ../nm_pepB_snapshots/
> > #
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > #
> > COMPT ../ab_pepB.top
> > RECPT ../ab.top
> > LIGPT ../pepB.top
> > #
> > GC 0
> > AS 0
> > DC 0
> > #
> > MM 0
> > GB 0
> > PB 0
> > MS 0
> > #
> > NM 1
> > @NM
> > DIELC 4
> > MAXCYC 1000
> > DRMS 0.1
> >
> > The calculation stops at sanmin_rec.8.out with the following error:
> >
> > 4. RESULTS
> > --------------------------------------------------------------------------------
> >
> > ---------------------------------------------------
> >
> > eedmeth=5: Using 1/r dielectric
> >
> > ---------------------------------------------------
> > Frac coord min, max: 0.131100379560032 1.07346184405983
> > The system has extended beyond
> > the extent of the virtual box.
> > Restarting sander will recalculate
> > a new virtual box with 30 Angstroms
> > extra on each side, if there is a
> > restart file for this configuration.
> > SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> > Atom out of bounds. If a restart has been written,
> > restarting should resolve the error
> >
> > If I understand correctly, sanmin_rec.in only does a local
> > minimization on the receptor (keep the conformation induced by the
> > ligand). Therefore there is a possibility that this receptor
> > is very unstable by itself. Is this why I get the error? If so, how do
> > I deal with it? Thanks.
> >
> > Eric
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