Hi Leila,
> I use Amber10. Thus, it's would better to do simulation in multiple steps.
>
> Is it true?
yes, Amber10 doesnt have the softcore-electrostatics needed for
single-step transformations. You could of course get Amber11 (or 12) :-)
> What points are important in free energy calculation for process such
> as DNA mutation and should be considered?
This question might be a bit to general to be answered in a concise email.
I am always happy to help with actual simulation problems and questions,
but this is knowledge that you have to build from experience of doing
simulations.
> 1) In your and other cases, there is only one change. But in my case,
> there is two changes
> (G to A and C to T). How to manage this case?
well, viewed differently, this is just one big change, So doing it all in
one go may be feasible. Check out publications from people who have done
DNA free energy mutations before, similar to what you plan, to see what is
possible.
> 2) If I only consider mutation of the G to A (both of G and A are
> pyrimidine), difference of G and A is as follows:
[...]
> is it true?
your table looks ok on first glance, but again, these are actual research
questions that I cant remote-solve in a minute. You have to work out and
verify your approach by actually trying out things.
Not to discourage you, but if no one in your group has previous knowledge
on how to do free energy calculations, then starting with the very complex
case of a DNA-basepair change is quite an undertaking.
Kind Regards,
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Dec 05 2011 - 04:30:03 PST
