AMBER Archive (2008)

Subject: RE: AMBER: united atom force field

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Tue Aug 26 2008 - 18:11:47 CDT

Adrien,

Unfortunately, antechamber cannot generate a UA prepin file for you … Dr.
Junmei Wang may comment on this … I believe the choice of force fields for
antechamber is only for the atom types.

If you read the Amber ff03ua paper, it is really not very hard to follow.

1) Run RESP with your QM ESP files by setting all nonpolar hydrogen charges
to zero.
2) Fit VDW parameters by running a few TI simulations. You may borrow these
parameters from ff03ua if you use the b3lyp/cc-pvtz charges as in ff03ua/aa.
3) The last step would be to fit torsion terms that are missing. If you have
a good AA template, it’s quite fast to do because the most expensive part is
the potential energy scan of a chosen torsion angle. Here you only need to
compute energies in your chosen AA model, which is much faster than the
usual QM approach. If you don’t have any good AA template, you’ll have to
compute the energies in QM.

All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Adrien Delmont
Sent: Friday, August 22, 2008 12:17 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: united atom force field

Dear Luo,
 
Thank you very much for your attention. If  I use ff03ua force field, run
Antechamber ( like in TUTORIAL B4 ) in order to generate prepin file with
doing the same procedure and write my own UA force field parameters in
frcmod file Will I have used the United atom force field that I'm planning
to use for n-alkanes  ?
Thanks in advance
 
Adrien
----- Original Message ----
From: Ray Luo <rluo_at_uci.edu>
To: amber_at_scripps.edu
Cc: rluo_at_uci.edu
Sent: Friday, August 22, 2008 8:37:38 PM
Subject: Re: AMBER: united atom force field

Adrien,

There is the ff03ua UA force field in Amber 9 and 10, but it was
developed for proteins. There is no general UA field field planned in
Amber. However, you can certainly follow the ff03ua strategies to
develop your parm/prepin files for n-alkanes.

All the best,
Ray
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