This might be a good use of the "AddToBox" utility; you can download it from
http://ambermd.org/tutorials/advanced/tutorial13/XtalTutor1.html
(it's the first link, hiding in the second paragraph). That archive
contains a lot of different things, but if you follow
http://ambermd.org/tutorials/advanced/tutorial13/Solvation.html
you should be able to run AddToBox to insert whatever number of waters you
want. They won't be in any equilibrated conformations, but I'd argue that
no equilibration matters if you're tiling the pre-equilibrated box around
some arbitrary solute and then clipping away waters that clash.
AddToBox can handle any unit cell shape; it takes PDB files of your solute
and a model of your solvent particle as input and returns a PDB file of
the whole system.
Dave
> Hello,
>
> I want to solvate a graphite surface according to its shape.
> Because angles are 90, 90, 120, the simple solvaetbox command in leap
> ----------------------------------------------------------
> source leaprc.ff99SB
> source leaprc.gaff
> loadamberprep c2.prepi
> loadamberparams c2.frcmod
> gr=loadpdb 40.pdb
> bondByDistance gr 1.5
> savepdb gr 40amb.pdb
> solvatebox gr TIP3PBOX {0 0 20}
> saveamberparm gr c40.prmtop c40.inpcrd
> --------------------------------------------
> can make the extra water space along in the xy plan(see the image file).
> Do you think it is possible to make a triclinic PBC box instead of the
> cubic box from leap?
> Thank you.
> Bongkeun Kim
>
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Received on Fri Oct 22 2010 - 11:30:03 PDT
