AMBER Archive (2006)

Subject: Re: AMBER: setBox with buffer in leap

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Mon Dec 11 2006 - 23:08:38 CST

Hi,

On Thu, 7 Dec 2006, Steven Winfield wrote:

> 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.

There is a bug in commands.c.
The third argument of the setbox command is not being used.
Bugfix 25 has been created and someone will put it on the web soon.

thanks for reporting this,
Scott

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