Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex

From: Thomas Cheatham <>
Date: Thu, 11 Mar 2010 20:21:51 -0700 (Mountain Standard Time)

> Hi. I am following the DNA tutoring and found that when using nucgen to
> build a DNA duplex the force field ff99 one gets a bad result but using ff03
> everything is OK. What is the problem.

"bad result" does not help me determine what the problem is; it is very
difficult for us on e-mail to understand what "bad result" means...

[Also, note that ff03 is a protein force field. There is no
ff03 nucleic acid force field.]

What force field is loaded (for the nucleic acids) likely depends on the
choice of leaprc file that is loaded, assuming you used the various AMBER
tools to build your system. We cannot help without more information;
which DNA tutorial, which version of AMBER, and what are the errors?

The tutorials serve an excellent purpose; try to reproduce what they are
doing. If you cannot, give us more information to help decipher what is
possibly going wrong so either we can fix a bug or fix the tutorial to
make it more clear...


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Received on Thu Mar 11 2010 - 19:30:05 PST
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