[AMBER] closeness

From: Sylvester Tumusiime <stumusii.uno.edu>
Date: Fri, 5 Dec 2014 05:12:36 +0000

   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
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