AMBER: amber: parameters for 5' nucleotide monophosphates

From: Jeff Schwinefus <>
Date: Mon, 13 Oct 2008 12:52:55 -0500

Amber community:

I apologize if this has already been asked, but do parameters for
isolated 5' nucleotide monophosphates (net charge = -2) exist? I have
been unable to find any information about these nucleotides in the
reflector archive, Amber website, and Amber manual. The closest
structures to what I want are the DA3, DC3, ..., RA3, RC3, ...
nucleotides in Amber, but they lack the proper phosphate structure and
charge for isolated nucleotide monophosphates.

If these isolated nucleotides monophosphates need to be designed similar
to tutorial #A1, by chance do parameters and RESP charges exist for
methyl phosphate (-2 charge) exist? I have searched the REDDB, but I
have not found any information for this ion.

Thank you for your time.

Jeff Schwinefus
St. Olaf College
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Wed Oct 15 2008 - 05:08:20 PDT
Custom Search