AMBER Archive (2009)

Subject: [AMBER] Re: ATP/GTP parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Dec 09 2009 - 00:51:03 CST

Hi Eduardo,

> some time ago you sent to me mol files for ATP and GTP (dXYP{1,2},
> XYP{1,2} ), I was wondering if you also have equivalent library files
> with charges for ATP and GTP, AND two hydrogens added at the gamma
> phosphates (will use with ff03) . . . I would appreciate this a lot.

You want:
       O
   R-O-P-OH right ?
       OH
Is it possible - I mean in biology ?

No we do not have it. However, I can explain you how to generate
charges for this fragment if this is the one you need. The idea would
be to generate something compatible with all what we have done...

regards, Francois

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