AMBER Archive (2006)

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

From: FyD (fyd_at_u-picardie.fr)
Date: Sat Aug 12 2006 - 14:09:29 CDT

Quoting a a <patd_2_at_hotmail.com>:

> 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:
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-59/
   with corresponding RESP inputs:
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-59/input1.in
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-59/input2.in

http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-58/
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-57/

Derivation of DNA FF topology database
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-45/

Derivation of DNA + RNA FF topology database
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-60/

regards, Francois

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