AMBER Archive (2009)

Subject: Re: [AMBER] RE:xleap problem

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Jan 27 2009 - 09:18:53 CST

On Mon, Jan 26, 2009, oguz gurbulak wrote:

> I'm now on Windows so I can only use rar or zip format for
> compressing files.

This is hardly true....just Google for "gzip windows" for example.

> the mail. I used packmol in order to get my pdb file that includes 100
> n-dodecane molecules. I added TER cards between each seperate n-dodecane
> molecule with using a script. You can examine my packmol pdb file attached
> to the mail.

You need to use the "set" command in LEaP to add the box information
after you load the packmol pdb file.

Also note: a box size of 9 Ang or so is too small for Amber. The box
size has to be at least twice the cutoff, so as a practical matter, the
smallest box that really works is about 18 Ang.

...dac

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