AMBER Archive (2009)

Subject: Re: [AMBER] Single Adenine

From: ros (
Date: Thu Aug 27 2009 - 11:27:06 CDT

Thank you very much for your answer! Actually, the interaction I am trying
to study is with an anti-cancer drug that has a Cu(II) atom. The metal is
coordinated with 2 glycinate molecules. We have X ray data of the
interaction between adenine and this copper-complex. I am trying to
reproduce this experiment using MD, so, the adenine with the drug will
interact non-covalently.

What do you think?

Have a great day!


2009/8/27 FyD <>

> 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. or
> R.E.D. Server 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 @
> 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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