Pantetheine Force Fields

While AMBER has built-in parameters for many components of a system, proteins with pantetheine-containing 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.