AMBER Archive (2009)

Subject: RE: [AMBER] Using AMBER force fields in NAMD

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Tue Apr 28 2009 - 17:45:15 CDT

> > I wish to use the AMBER98 force field for some MD studies, but already

If you've been using the CHARMM force field, you might as well use the
CHARMM-formatted AMBER force field files and use equivalent tools to
build. See Jeff Klauda's WWW site:

  http://terpconnect.umd.edu/~jbklauda/research/download.html

> There is no AMBER98 force field as far as I know, so I do not know what the

Yes, there is a parm98 and it was work that Piotr and I did!
JBSD 16, 845 (1999). parm99 is slight modification to this with nucleic
acids.

Moreover, contrary to Piotr's comments to the list, you cannot use the
same topologies since the dihedrals are indeed slightly different. You
can use the same -libraries- as ff94, but need the updated parameters.

If you are going to run DNA, I would recommend ff99SB+parmbsc0 (or on
Jeff's page, AMBER99-bs0).

With RNA, you can likely use either ff99SB or ff99SB+parmbsc0, however
both are not perfect. However, structures should stay together longer
than with the CHARMM all27 force field. Your mileage may vary.

p.s. do not forget the salt; as pointed out recently on the reflector and
subsequently verified by me, with no salt the RNA will become extended.

--tec3

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