[gmx-users] Creating topology for a small organic molecule

[Gunnar Widtfeldt Reginsson]

Hi.
I need to create a topology file for a small organic molecule that is to
interact non- covalently with a DNA duplex. I want to use the amber99 force
field.
I saw on this mailing list that you can use acpypi with antichamber to
create a topology for amber force fields. I got the amber10 tools and
installed but I couldn't find any more information on how to get the
antichamber package to work. I am finding this all very complicated since I
am not an expert in the unix language, so if anyone knows about a good
beginners tutorial on how to install antichamber and acpypi could you please
let me know were to find it.

Another question is, how difficult is it to create the topology for the
molecule by hand for the amber99 force field. Could someone please get me
started on that, if it would be easier. The molecule is a derivative of
cytosine.
I am using GROMACS 4 on Mac OS 10.5

Thanks.
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