AMBER Archive (2006)

Subject: Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next?

From: FyD (
Date: Sat Aug 12 2006 - 14:09:29 CDT

Quoting a a <>:

> I got to do the analysis for a fragement of DNA, with one of the DNA
> base pair with only PO2 remained. When I load the pdb file to xleap,
> it said it is not type, it seems that I have to define some parameters
> for it. What can I do? Can I use antechamber? Or are there any
> references values for the needed parameters that I could use?

You might be interested in looking in R.E.DD.B.

Derivation of new DNA nucleotides:
   with corresponding RESP inputs:

Derivation of DNA FF topology database

Derivation of DNA + RNA FF topology database

regards, Francois

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