AMBER Archive (2009)

Subject: Re: [AMBER] making leap to recognize 5' phosphate

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Jun 23 2009 - 02:45:31 CDT

Bala,

> Is there any way to make xleap recognize the 5' phosphate and create the
> topology.

I am note sure I understand your question. If you want a ff library
for the 5' phosphate you could use the dimethylphosphate molecule +
constraints during the fit to generate the corresponding molecular
fragment.

regards, Francois

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