AMBER Archive (2006)

Subject: AMBER: setBox with buffer in leap

From: Steven Winfield (
Date: Wed Dec 06 2006 - 18:43:58 CST

Dear all,

I'm trying to create an amino acid chain in a box with some vacuum
around it. Here is my the end of my leap.log file:

> chain = sequence { ALA SER GLY SER VAL LEU ALA }
Sequence: ALA
Sequence: SER
Joining ALA - SER
Sequence: GLY
Joining SER - GLY
Sequence: SER
Joining GLY - SER
Sequence: VAL
Joining SER - VAL
Sequence: LEU
Joining VAL - LEU
Sequence: ALA
Joining LEU - ALA
> setbox chain vdw 30.0
Box dimensions: 25.310469 17.748585 9.670358

As you can see, there isn't 30 Angstroms of clearance being left around
my molecule. Replacing 30.0 with { 30.0 30.0 30.0 } also fails. What am
I doing wrong? I'm using AMBER 9.


Steve Winfield.

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