AMBER Archive (2004)

Subject: Re: AMBER: "Total vdw box size" information is gone

From: David A. Case (case_at_scripps.edu)
Date: Sun Jun 27 2004 - 16:03:39 CDT

On Sun, Jun 27, 2004, Helios Chen wrote:

> Dear all, I used "solvatecap" command to solvate a protein and everything is
> o.k when I save the the topology and coordinate files by "saveAmberParm"
> command. But I have a question, why the "Total vdw box size" information
> are not appeared at last line in my coordinate file. I cann't do minimize
> by Sander because of lacking these. Are there any method to get them?

The solvateCap command does not create a periodic system, or any box
information. Use solvateBox or solvateOct if you wish to create a periodic
systems. If you wish to use your current prmtop file, you will need to
set ntb=0, to tell sander that this is a non-periodic system.

...dac

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