Hello,
I finally identified the origin of the problem: in "leap.in", I set "set
default pbradii bondi" which indicates implicit solvent, and I solvate
protein into water box, and in "min.in" I set "ntb = 1" which indicates
periodic boundary. These commands are not consistent with each other.
Thanks for your help and attention!
Xue
On Sun, Sep 19, 2010 at 5:07 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sun, Sep 19, 2010, xue wang wrote:
> >
> > I used the following leap.in file to prepare protein solvated into a
> water
> > box, and min.in to minimize protein structure together with water box.
> The
> > problem here is that, when I set "ntb = 0" (no periodic boundary) in
> min.in,
> > everything works fine. However, when I set "ntb = 1", min.out is empty
> > (containing nothing), no min.rst is generated and the program terminates
> > quick. Does someone have any idea on this? Thanks a lot!
> >
> >
> > *leap.in*
> >
> > 1. source leaprc.ff99SB
> > 2. set default pbradii bondi
> > 3. loadOff ions.lib
> > 4. loadamberparams frcmod.ions
> > 5. com = loadpdb 1POD.pdb0
> > 6. solvatebox com TIP3PBOX 12.0
> > 7. saveamberparm com pla2.top pla2.crd
> > 8. savepdb com pla2.pdb
>
> I think you must have filename confusion someplace. The pla2.top and
> pla2.crd
> files that you posted are for non-solvated, non-periodic system; I don't
> think
> they could actually have come from the commands listed above.
>
> I am unable to reproduce any sequence where there is no mdout file created.
> You might try simplifying the input file down to one that "works" (at least
> creates an error message), then try to figure out what lines trigger the
> behavior you report.
>
> In future reports, be sure to give the arguments to sander that your
> used...there might be something amiss there.
>
> ....dac
>
>
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Received on Mon Sep 20 2010 - 14:00:05 PDT
