AMBER Archive (2007)

Subject: AMBER: AMBER 9 - Force Field Options - Question

From: dpandit_at_brandeis.edu
Date: Tue Oct 16 2007 - 15:41:33 CDT

Hello AMBER Experts:
                     Before I ask my question about force field, I
would like to inform you that I am relatively new to AMBER and my
question is pertinent to proteins and I referred the links below. I
know there are some more discussions on force fields but the
conclusion was unclear.

Force field Discussions:

http://structbio.vanderbilt.edu/archives/amber-archive/2007/0663.php -
Suggests using ff99SB for proteins

http://structbio.vanderbilt.edu/archives/amber-archive/2001/0264.php -
Highlights issues with mix-matching force fields

Question:

I understand that force field selection is one of the most important
decisions a user makes for performing simulation. I understand
parameters , atom types and charges go hand in hand. However, as a
user even after reading the references it is not clear to me which
force field should I select for protein simulations from the options
below.

frcmod.ff03, frcmod.ff03ua, parm99EP.dat, frcmod.ff02pol.rl,
frcmod.ff99SB, frcmod.ff99SP

I am confused by the issue. Please help. Also feel free to let me know
if I missed something or if there are other references available.
Below I have listed major options from AMBER 9 manual.

Thank you.
Deepa

Options available from the Manual for proteins

Amber 2003 (Duan et al.) force field
frcmod.ff03 For proteins: changes to parm99.dat, primarily in the
phi and psi torsions.
all_amino03.in Charges and atom types for proteins.

Amber 2003 (Yang et al.) united-atom force field
frcmod.ff03ua For proteins: changes to parm99.dat, primarily in the
introduction of new united-atom carbon types and new
side chain torsions.
uni_amino03.in Amino acid input for building database
uni_aminont03.in NH3+ amino acid input for building database.
uni_aminoct03.in COO- amino acid input for building database.

Amber 2002 polarizable force field, and recent updates
parm99.dat Force field, for amino acids and some organic molecules;
can be used with either additive or
non-additive treatment of electrostatics.
parm99EP.dat Like parm99.dat, but with "extra-points": off-center
atomic charges, somewhat like lone-pairs.
frcmod.ff02pol.r1 Updated torsion parameters for ff02.
all_amino02.in Amino acid input ...
all_aminoct02.in COO- amino acid input ...
all_aminont02.in NH3+ amino acid input ....

all_amino02EP.in Amino acid input ...
all_aminoct02EP.in COO- amino acid input ...
all_aminont02EP.in NH3+ amino acid input ....

Amber 1999 (Wang et al.) force field, and recent updates
parm99.dat Basic force field parameters
gaff.dat Force field for general organic molecules.
frcmod.ff99SB "Stony Brook" modification to ff99 backbone torsions
frcmod.ff99SP "Sorin/Pande" modification to ff99 backbone torsions

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