AMBER Archive (2008)

Subject: AMBER: how to enlarge the TIP3PBOX size

From: Qiuting Hong (qiutinghong_at_gmail.com)
Date: Wed Sep 24 2008 - 17:56:10 CDT

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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