how to generate FF of DNA complex?

From: tang kwa <>
Date: Thu, 27 Mar 2003 07:43:47 -0800 (PST)

Dear all,

I have a problem with generating force field for
unusual molecule (DNA complex). The molecule is
3'-ApApApGpY-5' where A is adenine base, p is
phosphate group, and Y is a small molecule. A force
field of fragment 3'-ApApApG-5' endded with H5T atom
can be loaded from parm94.dat. Moreover, I have
generated force field of the molecule Y from

Because small molecule Y bonds to DNA by phosphate
group, so my problem is that I don't know how to
generate a topology file of this DNA-complex using
LEaP program because I don't have parameter for
linking atoms (phosphate group) between base G and
molecule Y.

Could you please give any advice? Thank you very much
in advance.

Sincerely Yours,

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Received on Thu Mar 27 2003 - 15:53:01 PST
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