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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Received on Fri Sep 26 2008 - 05:12:54 PDT
