Re: AMBER: Modified nucleotides

From: Sean Rathlef <>
Date: Mon, 12 Feb 2007 21:55:20 -0800

Hi Mathew,

I know auto-parameterization of (larger) organic compounds can be tricky, but there are scripts out there that will help. In my own opinion, partial charges are a fussy matter, because intuitively the electron density (and hence the atomic partial charges) involved will change as conformations (as in an MD simulation) change. Bayly's AM1-BCC charge model is good, but AM1 is outdated. If they had a PM6-BCC model, that would be something. Truth be known, assignment of partial charges is very tough when it comes to molecules that change shape. However, if you want a good energy reading from a force field, then partial charges will always be the focus. Let's face it - perfect partial charges (i.e., electrostatics) are the computational chemists dream. But if you run manipulated (as in molecular dynamic) structures, then even a supercomputer (which we tried) would have a very hard time computing the changes in charge distribution as changes in conformation were sampled (in a particular enseble, such as NPT for instance). The fact is, if man/woman wants to model molecules on computers, then the models just have to "feel" right, and this is not really an easy task. Also, if an "acceptable" partial charge ditribution is to be obtained, then realistically, one would want to model a structure (such as a protein, for instance) that is taken as a "snapshot" (as wouldoccur in a non-linear scaled mm-pbsa computation). AM1-BCC is a great model for partial charges, but having had some conversations with various experts on the ambiguity between gas and condences phases, I would speculate that an "idealized QM on-the-fly" partial charge model is still very far away. In my own opinion, AM1-BCC will do nicely as it encompasses molecular orbital features into the charge model itself, but the Amber developers may have a better idea than I do. Partial charges are magical, and that makes them all the more complex.


  ----- Original Message -----
  From: mathew k varghese
  Sent: Monday, February 12, 2007 8:44 PM
  Subject: AMBER: Modified nucleotides

  Dear AMBER users,

  I am planning to do some MD simulations of modified nucleic acids. Is it reasonable to use the am1-bcc charges for the modified nucleotides?

  Thanks in advance

  Mathew K Varghese
  Mathew K Varghese
  Research Scholar
  School of Pure and Applied Physics
  Kottayam, Kerala

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Received on Wed Feb 14 2007 - 06:07:33 PST
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