AMBER Archive (2006)

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

From: a a (patd_2_at_hotmail.com)
Date: Sun Aug 13 2006 - 23:29:59 CDT

Thank you very much Francois!

>From: FyD <fyd_at_u-picardie.fr>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What canI
>do next?
>Date: Sat, 12 Aug 2006 21:09:29 +0200
>
>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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