AMBER: running equilibration

From: Boutheina Kerkeni <>
Date: Sat, 8 Dec 2007 00:29:59 +0000

Hi Amber users

I have a couple of questions:
1) should I remove or keep crystallographic waters from my PDB file?
and add water using solvateoct
2)Does it matter the order of addions and solvateOct?

I want to run a minimization prior to MD on my protein.
3) I want to minimize all residues except the waters and ions (Na+),
how to specify this in GROUP input?

Hold the Protein fixed
RES, (?, ?)

Thanks for your help
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Received on Sun Dec 09 2007 - 06:07:45 PST
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