README.md

FEPrepare is NOT available as a stand alone program! To use FEPrepare please use FEPrepare web-server

FEPrepare

FEP prepare automates the set-up procedure for performing NAMD/FEP simulations.

Pre-requirements

Install VMD

Align your ligands and protein

The code used in FEPrepare is described below.

a) names3.py ensures consistency between the atoms of the ligands and it creates the following files: newligandA.txt, newligandB.txt, newligandArtf.txt, newligandBrtf.txt, newligandAprm.txt, newligandBprm.txt, how_many.

b) merge2.py identifies the common atoms between reference and mutant ligands. It returns sortedB, which is the .rtf file of the mutant ligand sorted according to the reference ligand.

c) dual2.py implements the dual topology methodology. It generates files where both ligands coexist (pdb: hybridpdb.txt, rtf: final.txt, prm: updated.prm)

d) complex.py generates a complex file where the hybrid ligand generated above and the protein coexist.

e) split_chains.py generates the psfgen file needed from VMD.

VMD commands:

f) vmd -dispdev text -e psfgen

g) if you would you like to add 150μΜ NaCl to your system:

vmd -dispdev text -e vmd_prepare_complex_after_gui_autopsf_ionize > vmd_log.txt

otherwise:

vmd -dispdev text -e vmd_prepare_complex_after_gui_autopsf > vmd_log.txt

h) vmd -dispdev text -e psfgen_solv

i) if you would you like to add 150μΜ NaCl to your system:

vmd -dispdev text -e vmd_prepare_ligand_after_gui_autopsf_ionize > vmd_log.txt

otherwise:

vmd -dispdev text -e vmd_prepare_ligand_after_gui_autopsf > vmd_log.txt

j) fep.py generates the necessary ionized_fep files for the simulation.

k) min-max.py returns the coordinates of the center of the box.