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

From: Nicolas Lux Fawzi <>
Date: Tue, 26 Jun 2007 08:16:54 -0700

Hi Professor Case,
Thanks for your response.
Yes, I really do have a 3 component system : multiple peptides (on the
order of 20), multiple organic solvent molecules (glycerol, which i
created in antechamber with gaff), and multiple waters.
I suppose I could make a pdb file with the correct ratio of glycerols
to peptides, replicate that manually/periodically enough times to get
the system size I want, then solvateBox to add the water. I was
wondering if there was an easier way that didn't involve manual placing
of all the peptides and organic molecules before solvating with water.


On Jun 26, 2007, at 8:08 AM, David A. Case wrote:

> 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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Received on Wed Jun 27 2007 - 06:07:36 PDT
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