schrodinger.application.desmond.fep_scholar_msj_generator module

class schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator(jobname, cd_params, structure_fname, force_field='OPLS_2005', ensemble='NPT', sim_time='5000', rand_seed='2015', complex_box_buffer_width=5.0, trj_interval=24.0)

Bases: object

This class generates master msj file that manages both solvent and complex legs of the FEP simulation.

__init__(jobname, cd_params, structure_fname, force_field='OPLS_2005', ensemble='NPT', sim_time='5000', rand_seed='2015', complex_box_buffer_width=5.0, trj_interval=24.0)

Valid FF : OPLS_2005 CHARMM AMBER

write_complex_msj()

write_solvent_msj()

write_master_msj()

generate_subjob_msj(fname, buffer_width, MSJ_TEMPLATE=None)

generate_master_msj()

modify_multisim_stage(raw)

Method modifies ‘multisim’ stage in the master msj file

get_total_proc()

static set_box_buffer_width(raw, width)

set_ff(raw)

set_lambda_hopping(raw)