AMBER Archive (2006)

Subject: Re: AMBER: a question about "solvateoct" in AMBER 8

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Apr 21 2006 - 13:48:01 CDT

> I found out that the box size information listed in XLEAP after add the
> solvent is different with that in ".inpcrd" file.

> solvateoct a TIP3PBOX 10.0
>Scaling up box by a factor of 1.371926 to meet diagonal cut criterion
> Solute vdw bounding box: 34.115 45.712 32.074
> Total bounding box for atom centers: 73.150 73.150 73.150

> Last line in ".inpcrd" file:
> 64.2159170 64.2159170 64.2159170 109.4712190 109.4712190 109.4712190

The boxes reported in the execution of the cmd are for an enclosing
rectilinear box, while the dimensions of the final inpcrd octo box
with 109-degree angles are probably the distances between the faces
created by chopping off the corners of the rectangular box.

Bill
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