AMBER Archive (2009)

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

From: FyD (
Date: Tue Jun 23 2009 - 04:48:34 CDT

Dear Bala,

> Sorry for not being clear. I have to simulate a DNA bound to a protein.
> Usually xleap doesnt recognize the phosphate at the 5' end of nucleic acid.
> But i want to consider this 5' phosphate during simulation. All i understand
> from previous postings is that i should create a new residue with 5' P and
> load its ff and prepin files to make xleap recognize the residue. But i dnt
> know how to do it. Could you please write me how can do the same.

ok you want to develop a FF library for a connecting group between a
proteine and an oligonucleotide. You might have to develop a new
fragment for your oligonucleotide, a new fragment for your protein and
a new fragement for your connecting group.

This is difficult to answer without looking at your structure...

regards, Francois

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