AMBER Archive (2008)

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

From: Qiuting Hong (qiutinghong_at_gmail.com)
Date: Fri Sep 26 2008 - 02:28:53 CDT

Hi,

Thank you for your information.

I use solvateoct 1wgg TIP3PBOX 10.0, and xleap said:

solute vdw bounding box: 36.162, 30.853, 52.074
.....
...
Density 0.877g/cc
added 6994 residues

I did run ptraj with the center command to reimage the water. However, I
still see the tip of side chain is out of the box.

Actually, when I prepare the sander input file, I also try solvateoct 1wgg
TIP3PBOX 12.0. The solute vdw bounding box is also: 36.162, 30.853, 52.074
(the density, and number of water molecules added is different). Thus,
I decide to use TIP3PBOX 10.0 since it has less water molecules.

Qiuting Hong

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