[gmx-users] QM guy at wits' end

[David van der Spoel]

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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> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se