AMBER Archive (2007)

Subject: Re: AMBER: set up system solution with 3 different components, each with multiple copies

From: David A. Case (case_at_scripps.edu)
Date: Tue Jun 26 2007 - 10:08:50 CDT

On Thu, Jun 21, 2007, Nicolas Lux Fawzi wrote:

> Could someone point me to a tutorial or any other info regarding
> setting up simulation system consisting of:
> multiple copies of short caped amino acids (ACE-X-NME) [ how do I get
> multiple copies of peptide in a system?

> multiple copies of a GAFF/antechamber-built organic co-solvent built
> from a single pdb file

The most straightforward approach would be to have a pdb file with multiple
copies of the organic molecule, and then use the solvateBox or solvateOct
commands to add the water. But maybe I don't understand your question:
do you really have three components: some peptides, an (unspecified) organic
solvent, and water?

....dac

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