From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Sat Feb 24 2007 - 14:33:16 CST
You may want to try to parametrize your own charmm type residues. Check the
references in the topology/parameter files for the procedure. You may want
to look at this paper, too:
"CHARMM force field parameters for simulation of reactive intermediates in
native and thio-substituted ribozymes", Evelyn Mayaan, Adam Moser, Alexander
D. Mackerell Jr., and Darrin M. York J. Comput.
Chem.<http://www3.interscience.wiley.com/cgi-bin/jhome/33822>,
28, 495-507, (2007).
there are some new charmm parameters developed for phosphate hydrolysis,
that may be of interest mainly from the point VdW radii point of view, if
you are trying to get solvation energies.
all the best
On 2/24/07, Pawel Weronski <pawel_at_lanl.gov> wrote:
>
> Dear NAMD experts,
>
> I would like to use the phosphate ions H2PO4(-1) and HPO4(-2) in my
> simulations. Is it possible to find the CHARMM force field parameters
> for them? I found the parameters on the web site
> http://www.colby.edu/chemistry/webmo/mointro.html but I am not sure if
> they are fine for computations with NAMD.
>
> Best,
>
> Pawel
>
>
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