AMBER Archive (2003)

Subject: equilibrated solvent box

From: pu xuemei (pxmscu_at_hotmail.com)
Date: Mon Jan 20 2003 - 02:54:33 CST

Dear amber user
I am simulating one enzyme in organic solvent using amber, the enzyme
contains 240 residues. For example, hexane is taken as solvent. I already
performed hexa.lib( hexa denotes hexane). In xleap, I solvate the enzyme
using solvatebox command:
 solvatebox enzyme HEXA 10.0 (HEXA is variable name of hexa.lib)
935 hexane molecules are added in box.The box size is 76.5 68.3 64.6. after
I finished 20ps equilibration with constant pressure, the box size is
shrinked to 67.4 60.1 57.7. the box is shrinked about 7-8 angstrom. I worry
about if box cell is too close to solute(enzyme) and if there are serious
bondary effect presented? which would influence the acceptablity of the
simulation results?
 so I want to add more hexane molecules on condition of no increasing box
size too much ( I afraid that too large boxsize lead to simulation died).I
use smaller closeness than 1 angstrom in solvating, but which can not add
enough hexane( up to 1000 molecule at most).
  The second question is if there are other command in xleap which can add
more solvent without increasing box size much?
  Maybe one equilibrated hexane solvent box can be one solution to the
problem. In order to get one equilibrated solvent box, I do so in xleap as
follows:
  solvatebox HEXA HEXA 10.0 (using hexane as solute and solvent)
  saveamber HEXA prmtop inpcrd
then equilibrate the solvent box in constant pressure.But I don't know how
to do next step,in other words, how I convert the restart or trajectory
file to parameters file (like WATBOX216) so that I could solvate enzyme
using the equilibrated solvent box in continuing work.
The third question is how to get equilibrated organic solvent box?
Any suggest and any help is very appreciated.
Thanks in advance
pxm

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