03 - tleap¶
Prerequisite(s): 02-protein-prep
run_tleap is used to prepare the topology and coordinate files.
Force fields¶
Protein¶
TODO:
Water¶
TODO:
Ions¶
TODO:
Chromophore¶
The eGFP chromophore is a non-standard residue that requires external parameters.
We use parameters from this paper that were parameterized with quantum chemical calculations. They provide frcmod.xFPchromophores.2022 and xFPchromophores.lib.2022 that allow us to run classical simulations in Amber. We use the following commands to load in these files.
# Assumes we are in a directory inside of a data directory
add_lines_tleap:
- 'addAtomTypes { {"cc" "C" "sp2"} {"cd" "C" "sp2"} {"cf" "C" "sp2"} '
- '{"c" "C" "sp2"} {"nd" "N" "sp2"} {"nc" "N" "sp2"} {"ne" "N" "sp2"}'
- '{"nf" "N" "sp2"} {"ha" "H" "sp3"} {"oh" "O" "sp3"} }'
- "xFPparams = loadamberparams ../../../methods/03-tleap/cro/frcmod.xFPchromophores.2022"
- "loadOff ../../../methods/03-tleap/cro/xFPchromophores.lib.2022"
Ions¶
TODO:
cation_identity: Na+
anion_identity: Cl-
neutralize_charge: true
extra_cations: 0
extra_anions: 0
solvent_ionic_strength: 0.150
To determine the appropriate atom and residue names for ions, you can inspect the ~/miniconda3/envs/metalflare-dev/dat/leap/lib/atomic_ions.lib file.
You will find a line starting with !entry that then specifies the residue type.
For example, !entry.CU1.unit.atoms specifies information for the residue name CU1.
Note that case matters!
Cu1 is not equivalent to CU1.
!entry.CU1.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"CU" "Cu+" 0 1 131072 1 29 1.000000
The following line(s) specify the types of atoms within this CU1 residue.
CU1 only has one atom called CU; thus, our PDB files should have a line like this
Solvent¶
TODO: