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

From: case <>
Date: Thu, 11 Mar 2010 22:21:12 -0500

On Thu, Mar 11, 2010, Qinqin Ji wrote:

> 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.

Wow. You leave a lot unsaid, but doing some "mind reading":

1. I'm guessing that you may be using an old tutorial(?) The revised version
of tutorial B1 no longer uses nucgen, since nucgen produces files with
outdated nomenclature.

2. the leaprc.ff03 file still uses the old (PDB version 2 nomenclature); this
is actually an oversight, but ff03 is primarily a protein force field, and
just copied ff99 files for nucleic acids.

3. leaprc.ff99SB or leaprc.bsc0 use the new nomenclature (PDB version 3), and
won't work well with nucgen.

But this is really a wild guess, since you don't say anything about what the
"bad result" is. But if I am correct, it may help clarify things.


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Received on Thu Mar 11 2010 - 19:30:04 PST
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