Dear Amber users,
I have a question concerning use of Tleap.
I want to build a cuboid box system containing a solvent and solutes.
I have a preliminary setup below:
source leaprc.ff99SB
WAT=SPC
loadAmberParams frcmod
loadamberprep pro4.prepi
a = loadpdb "x.pdb"
solvatebox a SPCBOX 10.0
saveamberparm a x.prmtop x.inpcrd
savepdb a x.pdb
quit
from the leap.log file, I get the following as the size and volume:
Total vdw box size: 34.015 41.102 44.674 angstroms.
Volume: 62457.939 A^3
Total mass 26186.398 amu, Density 0.696 g/cc
1. Should i consider the stated volume (62457.939 A^3) as the true volume
of the box? If not, what dimension can i use as a true reflection of my box
volume?
2. Secondly, I came across the "closeness" command in amber manual. Can i
use this in conjunction with the solvate (cap/box) commands to specify the
location of ions within my system as a substitute to the addions command and
the RP RW arguments of AddToBox?
Thanks,
S.T.
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Received on Thu Dec 04 2014 - 21:30:02 PST
