AMBER Archive (2007)

Subject: AMBER: running equilibration

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Fri Dec 07 2007 - 18:29:59 CST

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
500.0
RES, (?, ?)
END
END

Thanks for your help
Rerards
Boutheina
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu