AMBER Archive (2007)

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

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Thu Jun 21 2007 - 10:56:57 CDT

Hi
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 -- do I need a pdb file for each
configuration]
multiple copies of a GAFF/antechamber-built organic co-solvent built
from a single pdb file
multiple TIP3P or TIP4P water molecules. [how do I solvate these
multiple peptides with a two component solvent, part GAFF/antechamber
molecule and part standard water model]

I've looked through the leap section of the amber manual and can't
figure out an easy way to have a box with anything like this built.
Please let me know if you can assist with an example leap script?

Thanks
-Nick

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu