AMBER Archive (2008)

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

From: waqasuddin.khan_at_iccs.edu
Date: Thu Sep 25 2008 - 01:01:57 CDT

its very easy. just increase / change the numeric value (in angstorm as
default) in xleap interface. tban again check your explicit system

> 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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