VMD-L Mailing List

From: Caterina Bernini (caterinabernini_at_unisi.it)
Date: Tue Mar 31 2009 - 14:47:39 CDT

Dear VMD experts,

I would like to perform a MD simulation of a protein in a water box using
NAMD 2.6 and charmm force field.
My goal is to obtain a final equilibrated structure as a starting point
for further calculations of its spectroscopic properties (using DFT).
Since these spectroscopic properties are measured experimentally at pH 4.5
(0.1 M phthalate buffer) and at low Temperature (20 K), I was wondering
which are the best conditions for running molecular dynamics. Should I
perform the simulation at 20 K?
Then, regarding the pH, I know that the protonation state for a residue in
a particular protein may be different from the residue's protonation state
in solution. So, should I use an appropriate software to estimate the
protonation state of the amino acids in the protein? If so, could you
suggest me one?

Thanks in advance for your suggestions.

Best Regards,

Caterina 

-- 
Caterina Bernini, Ph. D. Student
Department of Chemistry
University of Siena
Via A. De Gasperi, 2
53100 Siena - Italy
Phone: +390577234232
Fax: +390577234254