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.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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Received on Tue May 10 2005 - 21:53:00 PDT
