AMBER Archive (2008)

Subject: Re: AMBER: Protein rotating out of box

From: Thomas Cheatham III (
Date: Wed Apr 02 2008 - 11:54:46 CDT

> Thanks for your comments. I guess the solvateoct is the way to go
> here. However, after I solvate using the command:
> 'solvateoct mol TIP3PBOX 15.0 0.78' parts of the solute is outside the
> box. Hmm.. Does not the buffer argument, in this case 15.0┼, specify
> the distance between the wall of the box and the closest atom? Or is
> it the distance to the walls in the cubic box, and then it shawes off
> the corners no matter if the solute is in the way? I have to make the
> buffer as high as 33┼ to get the solute entirely inside the box.

This is confusing to me as I never see such behavior... Just for kicks, I
just loaded up two long pieces of DNA duplex (both not centered at the
origin) and tried solvateoct unit TIP3PBOX 5.0 iso and also 5.0 0.78 and
the molecules are completely surrounded with water as expected (with a
minimum of 5A layer of water around the DNA). Note that if the system is
large, the PDB format can be blown so that not all the waters are visible.
How are you visualizing the solvation? What version of LEaP/AMBER?

-- tec3
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