# AMBER-FB15

Please see our paper at doi:10.1021/acs.jpcb.7b02320.

Note: If you downloaded files from this repository for running
simulations prior to the latest batch of commits on January 28, 2018,
the repo contained a pre-release frcmod.fb15 parameter file with an
error that could affect simulation results. The current version of
frcmod.fb15 in this repo is fixed. Also, the frcmod.fb15 files
distributed with ForceBalance and on SimTK have been correct
since the initial release.

This repository contains the following:

1) AMBER-FB15 protein force field parameters in Gromacs, OpenMM and
AMBER format, contained in "FinalParams".  These improved force field
parameters were derived using ForceBalance and recommended for use
with the TIP3P-FB water model (also included).

To use the new parameters in AMBER, run the following to install
the parameters.  Make sure AMBERHOME is set first:

> cd FinalParams/AMBER
> rsync -avz . $AMBERHOME/

To set up the system, make sure to source leaprc.fb15 instead of
leaprc.ff99SBildn.  It will automatically use the TIP3P-FB water model
as well.

To install the new parameters in GROMACS, run the following command
(it will install parameters to the GROMACS folder containing mdrun):

> cd FinalParams/GMX
> rsync -avz amberfb15.ff $(dirname $(which mdrun))/../share/gromacs/top

Now you can select the AMBER-FB15 and TIP3P-FB parameters from within
pdb2gmx.

To use the new parameters in OpenMM, make sure you have the
amber-fb15.xml file, then load the force field parameters using the
command: ForceField("amber-fb15.xml", "tip3p-fb.xml").

2a) 99sc-cnv.py, a Python script to convert the AMBER-FB15 protein
force field from the original Gromacs format that ForceBalance used

To perform the conversion, run:

> python 99sc-cnv.py Input/a99sc-v2-r1.itp

This will create new.xml, the OpenMM force field XML file.
for parameterization (contained in Input) to an OpenMM XML file

2b) oxml-aprm.py, a Python script to convert an OpenMM XML file
containing the AMBER-FB15 protein force field parameters to AMBER
format

To perform the conversion, run:

> python oxml-aprm.py FinalParams/OpenMM/amber-fb15.xml

This will create the AMBER force field files, leaprc command and
associated amino acid libraries.

Note that the solvent parameters are also needed to set up a
simulation, and these files are provided in FinalParams/AMBER.  This
is because TIP3P-FB is recommended for use with AMBER-FB15.

3) A script for checking the correctness of the AMBER conversion
(compared to the original GROMACS format where the conversion was
done).  This should be run in a folder such as 06.DHFRSol:

> python ../gmx-amber-compare.py protein.pdb

You may pass a "--ff" flag to the script, which selects between 'fb15',
'fb15ni', and 'ildn'.  The 'fb15ni' doesn't have any improper torsions
for the sake of making a clean comparison, since they are implemented
differently in AMBER vs. GROMACS.  The 'ildn' is just there as a reference
to make sure the comparison passes for an existing force field.

In order for these tests to work, the GROMACS and AMBER parameters
need to be installed, following the above instructions

molecule.py, nifty.py and PDB.py are bits of ForceBalance that are
used by the script.  Including them here removes the ForceBalance
dependency.