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ffAMBER
AMBER force field ports for the GROMACS
molecular dynamics suite
Maintained by Eric J.
Sorin, Ph.D.
Department of Chemistry &
Biochemistry
California State University, Long Beach
With significant contributions from:
Sanghyun Park Ph.D., Jory Z. Ruscio Ph.D., Erik Thompson*, and Kristin Haldeman*
(*CSULB undergraduate students)
Are you using our
ffamber ports for an upcoming publication? If so, please cite:
Sorin & Pande (2005), Biophysical Journal, 88, 2472-2493.
DePaul, Thompson, Patel, Haldeman, & Sorin (2010), Nucleic Acids Research,
38, 4856-4867.
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General Information:
We have ported the following AMBER potentials and TIP
water models for use in the GROMACS MD suite. AMBER
ports for GROMACS versions 3.1.4, 3.2.1, and
3.3/3.3.1 have been tested against AMBER 8.0, as
discussed below. As there have been several versions
of the TIP parameters published, we have taken them
from the most recent paper of the Jorgensen group to
describe TIP water (Mahoney, 2000). In addition to
these force fields, we have added several ions, the
urea molecule (URE), hydroxyproline (HYP), ornithine
(ORN), and diaminobutyric acid (DAB), as described
below. Please cite the following tabulated citations
when using any of these force fields.
AMBER conventions have been maintained where
possible. However, due to specific GROMACS
functionality this was not always feasible. As
detailed in this page, there are several very
important caveats to using these AMBER ports properly
within the GROMACS suite. Please
read the following information carefully before using
these AMBER ports, and refer also to the
ffAMBER FAQ
if you have questions that are not answered below.
This index.html and supporting files can be found in
the README subdirectory of the ffamber*tar.gz
downloads, which are available with or without the
pdf documentation listed in the table below.
Due to the caveats mentioned above, ffamber ports are
not yet distributed as part of the GROMACS package.
We are currently working with GROMACS developers Erik
Lindahl & David van der Spoel to make the
necessary changes in GROMACS that will allow us to
fully merge these ports with upcoming GROMACS
distributions and thereby simplify the use of AMBER
in GROMACS.
| Potential |
Port Name |
Literature |
DL |
| AMBER-94 |
ffamber94 |
Cornell et al.
(1995), JACS 117,
5179-5197 |
PDF |
| AMBER-96 |
ffamber96 |
Kollman
(1996), Acc. Chem. Res.
29, 461-469 |
PDF |
| AMBER-99 |
ffamber99 |
Wang et al.
(2000), J. Comp. Chem.
21, 1049-1074 |
PDF |
| AMBER-03* |
ffamber03 |
Duan et al.
(2003), J. Comp. Chem.
24, 1999-2012 |
PDF |
| AMBER-GS |
ffamberGS |
Garcia &
Sanbonmatsu (2002), PNAS
99, 2782-2787 |
PDF |
|
AMBER-GS-S** |
ffamberGSs |
Nymeyer &
Garcia (2003) PNAS 100,
13934-13939 |
PDF |
|
AMBER-99f*** |
ffamber99p |
Sorin &
Pande (2005). Biophys. J.
88(4), 2472-2493 |
PDF |
| AMBER-99SB |
ffamber99sb |
Hornak et. al
(2006). Proteins
65, 712-725 |
PDF |
| TIP3P |
HOH or T3P |
Mahoney &
Jorgensen (2000). J. Chem.
Phys. 112,
8910-8922 |
PDF |
|
TIP3P(heavy)**** |
T3H |
Mahoney &
Jorgensen (2000). J. Chem.
Phys. 112,
8910-8922 |
PDF |
| TIP4P |
T4P |
Mahoney &
Jorgensen (2000). J. Chem.
Phys. 112,
8910-8922 |
PDF |
| TIP4P-Ew |
T4E |
Horn et al.
(2004). J. Chem.
Phys.120, 9665-9678 |
PDF |
| TIP5P |
T5P |
Mahoney &
Jorgensen (2000). J. Chem.
Phys. 112,
8910-8922 |
PDF |
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* all-atom only, does NOT include the AMBER-03ua
united-atom potential
** no 1-4 vdW scaling
*** helix-coil force field
**** GROMACS heavy H2O definition using TIP3P
parameters
Force Field Information:
AMBER-94 is one of
the most widely used and understood of the seminal
all-atom force fields, though known to be somewhat
"helix-friendly."
AMBER-96 is a
variant of AMBER-94 in which peptide f/y torsional potentials have been
adjusted to yeild better agreement between molecular
mechanical and quantum mechanical energetics
(disfavoring helices, favoring extended
conformations).
AMBER-GS is
identical to AMBER-94 with peptide f/y torsional potentials removed (set
to zero). This AMBER-GS differs from Angel Garcia's
force field with a
minor modification: Garcia's version also does *NOT*
scale 1-4 vdW interactions (personal comm., A. Garcia),
as is standard for all AMBER force fields. Please note
this distinction when choosing between these force
fields [for more information, see Sorin & Pande
(2005). J. Comp. Chem. 26 (7),
682-690]. To use the "true AMBER-GS" force field that
removes 1-4 vdW scaling, which we have referred to as
AMBER-GS-S,
please use the ffamberGSs files provided in our ffAMBER ports.
AMBER-99 is the "3rd
generation" update to AMBER-94, including updated
parameters for both amino and nucleic acids. The
primary changes for peptides/proteins is again in the
f/y torsional potentials
(again to disfavor helical conformations).
AMBER-99f is our AMBER-99 variant
for helix-coil simulations and replaces the f torsion in AMBER-99 with that of the
Cornell (AMBER-94) potential.
AMBER-99SB is the
AMBER-99 variant developed by Simmerling and co-workers
with updated backbone f and
y torsions fit to ab initio
calculations (ported by Jory Z. Ruscio).
AMBER-03 is a
variant of the AMBER-99 potential in which charges and
main-chain torsion potentials have been rederived based
on QM+continuum solvent calculations and each amino
acid is allowed unique main-chain charges (nucleic
acids have not been modified from AMBER-99).
For more information on each of these FF's, please
refer to the AMBER homepage and the
references above.
The following additions have also been
made:
Ornithine (ORN) and diaminobutyric acid (DAB) residues
were defined using standard AMBER-94 and AMBER-99
Lennard-Jones and bonded parameters. ORN sidechain
charges were taken from the AMBER-99 port in TINKER
4.0; DAB sidechain charges were fit to maintain
proper LYS --> ORN --> DAB heavy atom charge
group trends, as described in:
B. Zagrovic, J. Lipfert, E.J. Sorin, I.S. Millett, W.F.
Van Gunsteren, S. Doniach, & V.S. Pande
(2005) PNAS, 102(33),
11698-11703.
The hydroxyproline (HYP) residue has also been added*
in accord to the following publications:
S.D. Mooney, P.A. Kollman & T.E. Klein
(2002), Biopolymers 64,
63-71.
S. Park, R.J. Radmer, T.E. Klein & V.S. Pande
(2005), J. Comp. Chem. 26,
1612–1616.
*due to the significant force field differences, HYP is
not present in AMBER-03 ports
The urea molecule (URE) was defined using standard
AMBER Lennard-Jones and bonded parameters, and RESP
charges were derived by Jim Caldwell.
The AMBER-94 and AMBER-99 force fields were ported and
validated first. Force field files for the variants of
AMBER-94 and AMBER-99 were then generated after
validation by making the minor modifications required
(i.e. peptide f/y and 1-4
vdW scaling).
While newer GROMACS distributions support multiple
torsional terms for a given atomic quartet, v3.1.4 did
not. Proper torsion potentials were therefore converted
to Ryckaert-Bellemans series in a fashion similar to
that described in the GROMACS manual for OPLS torsions.
Additionally, improper torsions are handled in GROMACS
using the proper dihedral definition to match the AMBER
standard, rather than the default analytical function
used for improper dihedrals in GROMACS. Because we
found inconsistencies in the definitions of improper
torsions when using the AMBER 8.0 package (i.e.
ordering of the atomic quartet), impropers in our ports
were set to agree with AMBER 8.0, and proper torsions
were then checked for exact agreement between all AMBER
8.0 Fourier series torsions and the GROMACS
Ryckaert-Bellemans series torsions.
To validate the potential energetics of our ports,
structures for all monomer, homodimer, and homotrimer
systems (including amino and nucleic acids) were
generated using the LEAP program in AMBER and these
structures were perturbed by adding a random number
between -0.2 and +0.2 Angstroms to all 3N coordinates.
This step is necessary because default structures
generated by AMBER's LEAP program contain many low
energy terms which are not suitable for quantitative
force field validation. All potential energy components
were compared between GROMACS 3.1.4/3.2.1/3.3/3.3.1 and
AMBER 8.0 and the resulting energy differences were
generally < 0.005%. These results were not
significantly altered by taking the mean over 10
independent perturbations for each monomer/dimer/trimer
system or altering the magnitude of the applied 3N
perturbations.
Mean relative errors for all
monomers, homodimers, and homotrimers*
(using single precision binaries)
| <|Error|>
(%) |
AMBER-94 |
AMBER-99 |
AMBER-03 |
| Amino |
Nucleic |
Amino |
Nucleic |
Amino |
Nucleic** |
| BOND |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
| ANGLE |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
| DIHEDRAL |
0.004 |
0.000 |
0.003 |
0.000 |
0.005 |
0.000 |
| 1-4 vdW |
0.000 |
0.001 |
0.001 |
0.001 |
0.000 |
0.001 |
| 1-4 QQ |
0.001 |
0.001 |
0.001 |
0.001 |
0.001 |
0.001 |
| vdW |
0.001 |
0.002 |
0.001 |
0.006 |
0.001 |
0.006 |
| QQ |
0.003 |
0.004 |
0.003 |
0.003 |
0.003 |
0.003 |
| Total Potential |
0.001 |
0.001 |
0.001 |
0.001 |
0.001 |
0.001 |
*highest mean error from GROMACS 3.1.4, 3.2.1,
3.3/3.3.1
**unchanged from AMBER-99, tested for consistency
| (1) |
Install the desired
GROMACS distribution
(v3.1.4, v3.2.1, v3.3, or v3.3.1). |
| (2) |
Download the
appropriate ffamber ports (.tar.gz) with or without
pdf documentation from the table below, being sure
that the version number you choose matches the
version of GROMACS you are using. |
| (3) |
Unzip/untar the
downloaded tar.gz file. |
| (4) |
Copy aminoacids.dat
and vdwradii.dat to the "top" directory in your
gromacs distribution (you should see force field
files there, such as ffoplsaa.*). If you plan on
simulating nucleic acids, refer to the note for nucleic acids in
aminoacids.dat below. |
| (5) |
Files for each force
field are located in a seperate subdirectory, such
as ffamber94/ for the Cornell potential. Copy the
desired ffamber* files to the top directory in your
gromacs distribution. |
| (6) |
Increment the number
at the top of the "top/FF.dat" file by 1 for each
AMBER port you'll install (so that it matches the
total number of forcefields available in the "top"
directory). |
| (7) |
Add lines like the
following to the "top/FF.dat" file. These are used
by pdb2gmx to allow you to identify the desired FF
and field 1 must match the ffamber* filename
prefixes, whereas the following fields can be
user-defined:
ffamber94 AMBER94
Cornell protein/nucleic forcefield
ffamber99 AMBER99
Wang protein/nucleic acid forcefield
ffamber99p AMBER99p
protein/nucleic forcefield
ffamber03 AMBER03
Duan protein/nucleic forcefield |
| (8) |
Locate the GMXRC in
your GROMACS distribution and run `source
GMXRC`. |
| (9) |
Run `pdb2gmx -H14 -f any.pdb` with any pdb to
verify that these force fields are now seen by
GROMACS. Working example .pdb files are available
below, alongside pre-prepared gro and top files (GROMACS 3.1.4
/ AMBER94) to which you can compare your
resulting files.
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| (10) |
Modify residue names
in your pdb file(s) as described below to properly
generate .gro and .top files using pdb2gmx (the
files above are ready to use). |
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AMBER port distributions
| Version |
Original
Release Date |
Download |
Notes on this
release |
| 3.1.4 |
July 2005 |
with pdfs
without
pdfs |
Must use -H14 flag in
pdb2gmx |
| 3.2.1 |
July 2005 |
with pdfs
without
pdfs |
-H14 flag no longer necessary
for pdb2gmx |
| 3.3 |
Nov. 2005 |
with pdfs
without
pdfs |
.hdb file format change,
hydrogen database now functional for nucleic
acids |
| 3.3.1 |
May 2006 |
with pdfs
without
pdfs |
This port has also been validated using GMX 3.3.3,
but may give warning or error messages using GMX 3.3.2 |
| 4.0 |
Feb 2009 |
with pdfs
without
pdfs |
This port has been validated using GMX 4.0.2, 4.0.3, 4.0.4 & 4.0.7
NOTE: pdb2gmx auto-converts residue CYM to CYN in 4.0.2 & 4.0.3 |
ffAMBER tar.gz files are ~7.5 MB with .pdfs and ~850 kB without
This list includes only the most important information
needed to properly use our AMBER ports inside the
GROMACS suite. Non-vital information is compiled in the
ffAMBER FAQ listed above. Information on
using GROMACS as well as FAQs, tutorials, and a user
forum are available at http://www.gromacs.org/.
| (1) |
(!) -H14 flag in
gromacs: You must use the -H14 flag
when running the GROMACS v3.1.4 version of
pdb2gmx to get *ALL* hydrogen-hydrogen 1-4
interactions that should be present in AMBER
topologies. This has been corrected in v3.2.1
and the -H14 flag is no longer necessary.
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| (2) |
(!) Residue
Nomenclature: Residues in the AMBER
ports are named according to their position in
the sequence (i.e. terminal, non-terminal,
monomer) following standard AMBER conventions.
For this reason, it may be necessary to rename
residues in the .pdb file you will import
beforehand. Please note that all residues are
named in the residue topology files (i.e.
ffamber*.rtp), so if you are unsure of the
correct residue name to use, you should be able
to find it there. The .rtp files are ordered as
follows: water models (TIP), ions & urea
(URE), peptide terminal capping residues (ie.
ACE, NH2, NMe), non-terminal amino acids (i.e.
TYR, ALA), non-terminal acidic amino acids
(i.e. ASH, GLH, etc.), C-terminal amino acids
(i.e. CALA, CGLY), N-terminal amino acids (i.e.
NALA, NGLY), and all nucleic acid residues.
Nucleic acids listed at the end of each .rtp
follow the following order for each residue
type: DNA is first, followed by RNA, in the
order 5'-term, 3'-term, non-terminal, and
monomer. The three .pdb files above are
examples of how pdb files shoud be modified.
Residues in the ffamber ports have been named
as follows:
| (a) |
Non-terminal amino and nucleic
acid residues follow standard
AMBER naming conventions. To avoid
confusion between GROMACS and AMBER
conventions, we have omitted the
redundant HIS residue, leaving HID,
HIE, HIP, and terminal versions of
these topologies. Additionally, due
to the automated changing of certain
residue names by pdb2gmx, the LYS and
CYS residues have been renamed LYP
(Lysine plus) and CYN (Cysteine
neutral, compared to AMBER residue
CYM = Cysteine minus).
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| (b) |
C- and N-terminal amino acids
include a C or N prefix respectively,
so C-terminal ALA is CALA and
N-ternimal PHE is NPHE. As with
non-terminal versions, the LYS and
CYS terminal residues are listed as
NLYP,CLYP and NCYN,CCYN.
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| (c) |
Nucleic acid residues come in
four flavors. All residue names
include XY, where X = D or R for DNA
or RNA respectively, and Y = first
letter of the nucleotide name. A
suffix (XYZ) is added
for monomers (Z=N), 5'-terminal
(Z=5), and 3'-terminal (Z=3)
residues. For example, 3'-term DNA
Cytosine = "DC3", 5'-term RNA
Cytosine = "RC5", non-terminal DNA
Cytosine = "DC", and lone RNA
Cytosine monomer = "RCN".
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| (d) |
Cys disulfide bonds can be
instituted by changing the names of
the CYS residues involved in the
disulfide bonds to CYS2.
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| (3) |
(!) Atom
Nomenclature: Once you have modified
the residue names in your pdb file according to
the rules above, pdb2gmx may report a fatal
error like "Fatal error: Atom AA in residue XYZ
not found in rtp entry with NN atoms while
sorting atoms." This may or may not be caused
by the use of an aminoacids.dat file in the
"top" directory of your GROMACS distribution
that does not include the name of the residue
that is causing the problem (XYZ in this case).
This can be easily fixed by modifying the name
of the problematic atom in your .pdb file to
match what is shown for residue XYZ in the .rtp
file.
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| (4) |
(!) Water
nomenclature: residues in
pre-solvated pdb files should be named as shown
here to use the correct water model in the
desired amber port: TIP3P ("HOH" or "T3P"),
heavy TIP3P ("T3H"), TIP4P ("T4P"), TIP4P-Ew
("T4E"), and TIP5P ("T5P"). This usage allows
any model to be used without modifying the
force field (.rtp) files. Note, however, that
for the default "HOH" listing the TIP3P model
will be is assumed. Also note that because
GROMACS supports SOL=HOH water definitions,
importing a solvated PDB with names other than
HOH or SOL may cause the solvent molecules to
be treated as part of the biopolymer rather
than listing SOL molecules at the end of the
topology, which has to be modified by hand
after the fact.
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| (5) |
(!) Specifying water
models in .top files: If not using
the default SPC water model in GROMACS, make
sure you list the correct ffamber_tip*.itp file
in your gromacs topology file! TIP3P heavy
water (H's four times heavier, difference
subtracted from oxygen) is defined in
ffamber_tip3p_heavy.itp, and the TIP4P-Ewald
model uses ffamber_tip4pEW.itp. All other
models are specified in the ffamber_tipXp.itp
files, where X = {3,4,5}. Water boxes are also
present, with the .gro file extension.
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| (6) |
(!) For nucleic acid
simulations: Amino acid residues
have been added to aminoacids.dat, which (i)
allows easy use of GROMACS analysis tools and
(ii) aids GROMACS in matching atoms in a pdb
with those in the residue topology (.rtp) file.
However, for nucleic acids this also often
causes pdb2gmx to replace an H atom in the
first residue of all nucleic acid chains with
an incorrect H atom, resulting in non-neutral
charge. The correct atom is generally replaced
with an atom of type amberXX_25 (hydroxyl H),
as pdb2gmx treats it as a terminal hydrogen.
For this reason, we provide both the standard
aminoacids.dat
(without nucleic acids) and a second version
with nucleic acid residues included ( aminoacids-NA.dat).
You can run gcaa.pdb
with both versions of aminoacids.dat by copying
either file into your "top" directory before
each trial and diff'ing the resulting top files
to see this difference. There are three ways to
handle this:
| (a) |
Include all nucleic acid names in
aminoacids.dat and correct the [ atoms ]
section of the resulting .top file by
hand/script after running pdb2gmx (both
the atom type and the charge). |
| (b) |
Remove nucleotide names from
aminoacids.dat before importing your pdb
file and add them back afterward to use
standard GROMACS tools. |
| (c) |
Do not include nucleic acid names in
aminoacids.dat and make an index file
which specifies the DNA/RNA atoms to use
standard GROMACS tools. |
|
|
Note that if you choose options
(b) or (c) above, you may need to
modify the atom names in your .pdb file to
agree with the residue listings in the .rtp
file due to issue (3) above.
|
| (7) |
(!) Using AMBER
ions: Our AMBER ports include common
ion definitions, which are listed in the
ffamber*.rtp files (just below the TIP water
models). This allows the AMBER ports to be used
without modification or use of the GROMACS
ions.itp file. At the moment these include
Cl- ,
IB+,
Na+,
K+ ,
Rb+,
Cs+,
Li+ ,
Ca2+,
Mg2+,
Zn2+,
Sr2+, and
Ba2+. If your pdb
file has ions present and pdb2gmx does not
properly convert those ions, please check the
atom and residue name of your ions and rename
them if necessary to agree with the .rtp file.
If you are using ion-related GROMACS tools,
such as genion, you will need to enter the
AMBER ion definition to the ions.itp file in
the "top" directory of the GROMACS
distribution.
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Being familiar with the AMBER family of force fields is
not necessary for the use of our ports, but it is
highly recommended. More importantly, we expect that
those using these ports will be very experienced in
using both GROMACS and UNIX/LINUX. Please do not
contact us with GROMACS/UNIX/LINUX questions.
We have done our best to provide very complete
documentation above to help GROMACS users with the
installation and use of our AMBER ports. Please do not
email with implementation questions unless you are
confident that your problem/question has not yet been
addressed above or in the associated ffAMBER FAQ.
Communications not answered above or on our ffAMBER FAQ should be directed to
Eric J. Sorin
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