AMBER Archive (2008)

Subject: RE: AMBER: how to enlarge the TIP3PBOX size

From: Ross Walker (
Date: Thu Sep 25 2008 - 09:55:38 CDT

Hi Qiuting,


I'm not sure I understand exactly what you want to do here. I assume you
mean you want to completely repeat the setting up of the system?


In this case you just change the size of the buffer than you specified for
the solvateoct command. E.g. if before you had:


solvateoct foo TIP3PBOX 8.0


then try


solvateoct foo TIP3PBOX 12.0


This will give you a 12 angstrom buffer instead of 8 angstrom.


How big was the original box you used? Are you certain your box is too small
and it is not just an imaging artefact that you are seeing? You could try
running ptraj with the center command and select the residues of your
protein as the center mask and then you might find that it is just an issue
with the origin location and you are really fine. However, it is hard to
comment further without seeing the actual system.


Good luck,


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