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

From: Ilyas Yildirim <>
Date: Fri, 12 Mar 2010 00:03:32 -0500 (EST)

I am not sure what the difference of old and new nomenclature is, but
creating a single strand using nucgen is pretty easy. Create a DNA duplex
where one strand is the single strand you want to build, and the other
strand being the full complementary strand. Then, just take the
coordinates of the single strand you want to use.

If there is a difference between the old and new nomenclature, then it
should be the way the pdb file is written. I use jmacs the edit the pdb
files so that leap will understand the atoms and the residues. You can
follow a similar method. If it is just a 22mer, you can do it by hand. I
am still curious how the old/new nomenclature can affect the preparation
of the prmtop/inpcrd files when leaprc.ff99SB is used.

Good luck,

   Ilyas Yildirim, Ph.D.
   = Hutchison Hall B#10 - Department of Chemistry =
   = - University of Rochester =
   = 585-275-6766 (office) - =
   = =

On Fri, 12 Mar 2010, Asfa Ali wrote:

> Hi,
> If nucgen produces files with outdated nomenclature, what should we use to
> create DNA duplex so that it works well with leaprc.ff99SB (which uses PDB
> Version 3)?
> Also I want to create a 22 mer single stranded DNA. What should I use?
> Thanks...
> Asfa.
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Received on Thu Mar 11 2010 - 21:30:02 PST
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