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 Sun Sep 19 2010 - 14:30:04 PDT
