AMBER Archive (2005)

Subject: AMBER: sander error

From: Yam (yamwaikeat_at_yahoo.com)
Date: Mon Oct 17 2005 - 21:10:50 CDT

Dear all,

Hello. Following some advises from fellow amber
friends, I have re-do the setting of the input files
(prmtop and crd files) with tleap. However, the same
problem still arrise when I try to run minimization.

| Flags: MPI
 getting new box info from bottom of inpcrd
 peek_ewald_inpcrd: SHOULD NOT BE HERE

The system contains about 1.4M atoms with octahedron
water and ions. And the attempting minimization is
only step no. 1, therefore setting ntx=1 (default)
(not even on MD runs). I have checked the last line of
my inpcrd file and is clear that the water box is
octahedron.
Anyone has any idea on what is going on? could it be
the limited number of atoms in sander? Please help.

regards,
Yam

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Tue, Oct 11, 2005, Yam wrote:
> >
> > Thanks a lot for the help. I have checked with
> both
> > prmtop and crd files, looks fine for me... but, to
> be
> > sure, I have re-run tleap to generate both files
> > (using the same protocol). Now, I have another
> problem
> > with minimization with sander:
> >
> > getting new box info from bottom of inpcrd
> > peek_ewald_inpcrd: SHOULD NOT BE HERE
> >
>
> We need more details. What value of ntx are you
> using? What kind of
> periodicity did you set up (rectangular or truncated
> octahedron)? If you
> set ntx=5 (or 7) but don't have any velocities in
> the inpcrd file, the program
> will probably be confused. But basically, you are
> not providing enough
> information for anyone to provide much real help.
>
> Try to see how your input files differ from those in
> the test cases (e.g.
> in amber8/test/dhfr or amber8/test/4096wat). Maybe
> that will help you figure
> out what is going wrong with your inputs.
>
> ...regards...dac
>
>
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