Date: Fri, 22 Oct 2010 10:39:04 -0700
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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(image/png attachment: c20w.png)
