AMBER Archive (2009)

Subject: Re: [AMBER] ATP and GTP parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Sep 03 2009 - 01:15:54 CDT

Eduardo,

> I was wondering if anyone can supply parameters for the phosphates XYP
> with X={A,G}, Y={T,D,M} other than those
> found in http://www.pharmacy.manchester.ac.uk/bryce/amber
> I heard somebody has the parameters compatible with ff03, would you
> care to share those?

ok no problem.

Do you need dexoxyribose or ribose ?
Which protonation state for each terminal phosphate ? -2 or -1 ?

regards, Francois

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber