AMBER Archive (2009)

Subject: Re: [AMBER] Single Adenine

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Aug 27 2009 - 02:05:54 CDT

Dear Ros,

> Thanks for the help! I have a single adenine working with parm and top files
> made from tleap.
>
> Quick question, what is the best way to add two molecules so they can
> interact?
> 1- Make a pdb with both molecules and then do all the fiddling of external
> parameters in tleap
> 2- Join somehow directly on tleap once each molecule has its external
> parameters loaded

Let's take two different examples:

-1) a polyanion such as an oligonucleotide neutralized by Na+ ions in
a box of explicite water molecules: here, each Na+ ion is not
covalently connected to a phosphate group. Na+ are present to
neutralize the system and are free to interact with phosphate groups,
with any other chemical groups and/or to be solvated.

-2) a metal complex such as heme with iron or your adenine-Cu2+
complex. You have two options here:

(a) You decide to make your adenine-Cu2+ complex not covalently
connected and the total charge of adenine and Cu2+ will be 0 and +2,
respectively. In this case, you can take the force field (FF) library
for adenine from the Amber FF topology database and create a FF
library for Cu2+ (as for Na+).

(b) You decide to make a covalent bond between adenine & Cu2+, the
total charge of Cu2+ will strongly decrease and you will have to build
a new FF library for this adenine-Cu2+ complex. Antechamber does not
handle metal complexes. You can use R.E.D.
http://q4md-forcefieldtools.org/RED/ or R.E.D. Server
http://q4md-forcefieldtools.org/REDS/ for that. In this case, you have
to carefully check that a connectivity between adenine and the metal
is present (if not added by Ante_R.E.D., add it manually) in the P2N
input file. See our tutorials @
http://q4md-forcefieldtools.org/Tutorial/. As you have a physical bond
between adenine & Cu2+, both components of your molecular system will
obviously remain connected during MD simulations.

regards, Francois

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