On 2013-11-20 20:07, SAllen wrote:
Hello,
I want to run MD simulations on a series of macrocycles that contain a lot
of non-standard residues (dehydroalanines, dehydrobutyrines, 1,3-thiazoles,
and a pyridine for good measure). I've been coming the internets for a
reasonable guide on how to develop parameter and topology files for my
structures, and I'll I've found are sites saying that it's too hard. Does
anyone have any good guides for developing (reasonable!) topology and
parameter files? I have access to lots of QM programs (gaussian, spartan,
even schrodinger).
You want to make polymers of those compounds?
For single molecules check http://virtualchemistry.org
How many you want to do? You can contact me off list if you wish, I have
1600 small molecules parameterized, but not tested yet.
Thanks,
-Scott
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