AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Sep 25 2008 - 01:40:21 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,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Qiuting Hong
Sent: Wednesday, September 24, 2008 3:56 PM
To: amber_at_scripps.edu
Subject: AMBER: how to enlarge the TIP3PBOX size

 

Dear amber users,

 

I am using TIP3PBOX to solvate ubiquitin. After the explicit water
simulation, I reimage the water back into the box, but find out part of the
ubiquitin side chain is out of the water box. I guss the box is too small.

I am trying to re-run the simulation. But I don't know how to change the
size of TIP3PBOX. I want to use solvateoct.

Can somebody help me out?

 

Qiuting Hong

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