Pantetheine Force Fields
While AMBER has built-in parameters for many components of a system, proteins with
ligands (PCLs) requires extra parameter files. These files can be found in the PFF library
created by Dr. Ray Luo at UCI. The PFF parameters have been charged with three
different methods: Gasteriger, AM1-BCC, or RESP. For more information, see
[Zhao et al.2021]. You can find his libraries for different PFF
here. Each PCL has PFF files compatible
with all three charging methods.
Note: For PCLs with both .frcmod1 and .frcmod2 files, both files need to be downloaded to correctly parameterize a simulation.
Example and More Tutorials
The following example shows how to load the PFF files to create a topology and coordinate file for use in AMBER. It assumes that you have already downloaded the OFF library and frcmod files for the AM1BCC method.
source leaprc.protein.ff19SB source leaprc.gaff2 source leaprc.water.opc loadamberparams PNS-BCC.frcmod loadoff PNS-BCC.lib mol = loadpdb file.pdb solvateoct mol OPCBOX 8.0 addionsrand mol Cl- 0 saveamberparm mol file.prmtop file.inpcrd savepdb mol file-bcc.pdb quit
You can find a tutorial on using PFF in Amber here.