AMBER Archive (2002)

Subject: solvateOct

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Fri Nov 22 2002 - 15:36:33 CST

I'm using the following procedure from the LEaP manual to set up a truncated
octahedron periodic box of SPC/E water:

"The normal choice for a TIP3 _solvent_ UNIT is WATBOX216, which is a snapshot
from a room-temperature equilibration for this model. If you want to solvate
with other water models (say TIP4P), try the following: (a) solvate the system
with WATBOX216, using the default TIP3 model; (b) use ambpdb to convert your
prmtop file to Brookhaven for-mat; (c) restart LEaP, choose the TIP4P water
model (instructions are in the Database chapter), then use loadPdb to bring
back in the system you have created."

Steps a-c went fine, but my question is how to get the box information back in
once the system has been reloaded with SPC/E chosen as water model. I imagine
if I were using a regular box, the setBox command would put the box back in
without changing the system. Is there something comparable for solvateOct?

Thanks,

Kristina

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu