On Mon, Feb 22, 2010, Jason Swails wrote:
> I'm not sure if what I'm seeing with sleap/tleap is supposed to be
> happening or not...
>
> When I run the following script:
> -----------------------------------------------------------
> source leaprc.ff99SB
> l = loadpdb GM2.pdb
> addIons l Na+ 0
> solvateOct l TIP3PBOX 15.0
> saveAmberParm l prmtop inpcrd
> quit
>
> -----------------------------------------------------------
>
> through sleap, ifbox in the prmtop is set to 1.
This is a bug....certain things (like wrapping, which I still don't like
to see inside sander), depend on the value of ifbox. Wei: solvateOct needs
to set ifbox to 2.
>
> through tleap, ifbox in the prmtop is set to 2.
This is the correct behavior.
....dac
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Feb 22 2010 - 13:30:03 PST
