Experiments

inputs/extras/extras_expts.py

{

'multiply':{
#####
'tags':[],
'script':'scripts/multiply.py',
'params':None,
'extensions':['*.py','../bilayers/codes/*.py'],
'settings':"""
step: large
requires: multiply
equilibration: npt-bilayer
proceed: True
genconf gap: 0.3
nx: 10
ny: 10
"""
},

}

inputs/extras/test_fast_expts.py

{

'table':{
#####
####
###
##
#
'quick':"""
import amx,shutil
shutil.copyfile(amx.settings.ready,amx.settings.store)
""",
},

'ultra':{
#####
####
###
##
#
'metarun':[
{'step':'bilayer','do':'bilayer_control','settings':"""
step: bilayer
monolayer top: 90
composition top: {'DOPC':0.64,'DOPS':0.16,'POP2':0.2}
composition bottom: {'POPC':1.0}
"""},
{'quick':'table','settings':"""
ready: s01-bilayer/md.part0001.gro
store: inputs/bilayer-cgmd-small.gro
"""},
{'step':'protein','do':'martinize','settings':"""
start structure: inputs/helix0.pdb
"""},
{'step':'adhere','do':'bilayer_protein_adhesion','settings':"""
force field: martini_upright_alt
sources: ['@martini/auto_ff/martini_upright_alt.ff']
placement method: banana
group up: resid 19
group down: resid 7
group origin: resid 7
bilayer structure: inputs/bilayer-cgmd-small-flat.gro
protein_lattice:|{
	'nrows':1,'ncols':1,
	'lattice_type':'square',
	'space_scale':20,
	'total_proteins':1,
	'protein_shift_up':1.0,
	}
"""},
]},

'bilayer288':{
#####
####
###
##
#
'metarun':[
{'step':'bilayer','do':'bilayer_control','settings':"""
step: bilayer
monolayer top: 144
composition top: {'DOPC':0.64,'DOPS':0.16,'POP2':0.2}
composition bottom: {'POPC':1.0}
thickness: 18
"""},
{'quick':'table','settings':"""
ready: s01-bilayer/md.part0001.gro
store: inputs/structure-repo/bilayers-cgmd/bilayer-cgmd-288.gro
"""},
]},

'enth-martini-demo':{
#####
####
###
##
#
'metarun':[
{'step':'protein','do':'martinize','settings':"""
start structure: inputs/structure-repo/proteins/1H0A-prepped.pdb
"""},
{'step':'adhere','do':'bilayer_protein_adhesion','settings':"""
force field: martini_upright_alt
sources: ['@martini/auto_ff/martini_upright_alt.ff']
placement method: globular_up_down
group up: all
group down: ['resid 1-22','resid 68-72']
group origin: ['resid 1-22','resid 68-72']
bilayer structure: inputs/structure-repo/bilayers-cgmd/bilayer-cgmd-288.gro
protein_lattice:|{
	'nrows':1,'ncols':1,
	'lattice_type':'square',
	'space_scale':20,
	'total_proteins':1,
	'protein_shift_up':1.0,
	}
"""},
]},

'ultra2':{
#####
####
###
##
#
'metarun':[
{'step':'bilayer','do':'bilayer_control','settings':"""
step: bilayer
monolayer top: 90
composition top: {'DOPC':0.64,'DOPS':0.16,'POP2':0.2}
composition bottom: {'POPC':1.0}
"""},
{'quick':'table','settings':"""
ready: s01-bilayer/md.part0001.gro
store: inputs/bilayer-cgmd-small.gro
"""},
{'step':'bilayer','do':'bilayer_control_flat','settings':"""
step: bilayer
monolayer top: 90
composition top: {'DOPC':0.64,'DOPS':0.16,'POP2':0.2}
composition bottom: {'POPC':1.0}
"""},
{'quick':'table','settings':"""
ready: s01-bilayer/md.part0001.gro
store: inputs/bilayer-cgmd-small-flat.gro
"""},
{'step':'protein','do':'martinize','settings':"""
start structure: inputs/helix0.pdb
"""},
{'step':'adhere','do':'bilayer_protein_adhesion','settings':"""
force field: martini-sources
sources: ['@martini/martini-sources.ff']
placement method: banana
group up: resid 19
group down: resid 7
group origin: resid 7
bilayer structure: inputs/bilayer-cgmd-small.gro
protein_lattice:|{
	'nrows':1,'ncols':1,
	'lattice_type':'square',
	'space_scale':20,
	'total_proteins':1,
	'protein_shift_up':1.0,
	}
"""},
{'step':'protein','do':'martinize','settings':"""
start structure: inputs/helix0.pdb
"""},
{'step':'adhere','do':'bilayer_protein_adhesion','settings':"""
force field: martini_upright_alt
sources: ['@martini/auto_ff/martini_upright_alt.ff']
placement method: banana
group up: resid 19
group down: resid 7
group origin: resid 7
bilayer structure: inputs/bilayer-cgmd-small-flat.gro
protein_lattice:|{
	'nrows':1,'ncols':1,
	'lattice_type':'square',
	'space_scale':20,
	'total_proteins':1,
	'protein_shift_up':1.0,
	}
"""},
]},

}

inputs/extras/structures_expts.py

{

'helixer':{
#####
####
###
##
#
'tags':['cgmd'],
'script':'scripts/coiled_coil_linker_dev.py',
'params':'@bilayers/parameters.py',
'extensions':['geometry_tools/*.py','@bilayers/codes/bilayer.py'],
'settings':"""

USAGE NOTE:|
	this creates a coiled-coil structure (the "helixer" name is clumsy)

step: helix
sequence:|
	TIPFAPLSQSKTSHGVSLSIVMEGDYRDSQYTTSYPIDKRHGGSFSADTRQAVTGSESHT
	LKDPETNPLVLNREFTIQEDDKDPIQLKVTPLKDNKSRYYIGSFEPRCLALLFVEYTIAC
	PILLLQSRAGDVEVRRPEGIESGALLHHRMLSIMMVLQLDEPKLFSLPEKDYIKTFGDDS
	LISEVRLKQVAELAEILIGKNQYYETIQSFLQYVASEKRKLKVLKMERFAVGSMIASNIF
	EPLSQKKRLEVASLYYIKSFLCYIKNPYDELRRKADLHTIESAMKSAILSVQDVSGHDRT
	GDKFKKQDINNNEAPLSLVKFLQRMFEEDGYPNKEVESLERALKSNILKYQCSKFAYPTG
	TKDLVNADDKHKEEDQQDEKHADREQSTDLLEKTFVAHMVVESELLRSELFSQPKQRREN
	RSSGHELRKLPGKVAQSLQAVSFMDEHSIQTYVEIISLTKNNMAILNPLNENFDTKLSES
	SIATKLELRIEKILMAAGTIISPKNASDARVPGEQGKIIVLDAEDDSISELFYYKQTVNF
	SSDYRKLRKSIHTWETQSQFRQEQSLINRELVVVLITYIRALGFAKLQENDQDIRNSDME
	VLYDPTKLQVWVPTKKEWIHLKSQMEIVISITNEKTERRAQPQLVKEHLRPQQ
secondary structure: ''.join(['H' for i in range(1,90+1)])
sequence slice: "1-90"

#---assume an ideal coiled coil
oligomer specs:{'n_coils':2,'anti':True,'residue_shift':0}

residue_library: @martini/library-residues
sources: ['@martini/martini-sources.ff']
files: ['@martini/library-general-structs/martini-water.gro']
force field: martini-sources
review 3d: false
backwards script: @martini/bin/backward/backward.py
solvent: martini-water
martinize script: @martini/bin/martinize.py
atomistic force field: charmm27
ionic_strength: 0.150
water: tip3p
sol: W
cation: NA+
anion: CL-
equilibration: short
water edges: [2,2,5]

mdp specs:|{
    'group':'cgmd',
    'mdps':{
        'input-em-steep-in.mdp':['minimize'],
        'input-md-short-eq-in.mdp':[{'nsteps':1000000,'groups':'protein-water',
        	'temperature':'protein-water','dt':0.001}],
        'input-md-in.mdp':[{'nsteps':10000000,'groups':'protein-water',
        	'temperature':'protein-water','restrain':'posre-com-only','pressure':'standard-isotropic'}],
        },
    }

"""},

'coiled_coil_only':{
#####
####
###
##
#
'tags':['cgmd'],
'script':'scripts/coiled_coil_only.py',
'params':'@bilayers/parameters.py',
'extensions':['geometry_tools/*.py','@bilayers/codes/bilayer.py'],
'settings':"""

USAGE NOTE:|
	forked from "helixer" to create the helix without solvent
	meant to precede a flat-bilayer routine

step: helix
sequence:|
	TIPFAPLSQSKTSHGVSLSIVMEGDYRDSQYTTSYPIDKRHGGSFSADTRQAVTGSESHT
	LKDPETNPLVLNREFTIQEDDKDPIQLKVTPLKDNKSRYYIGSFEPRCLALLFVEYTIAC
	PILLLQSRAGDVEVRRPEGIESGALLHHRMLSIMMVLQLDEPKLFSLPEKDYIKTFGDDS
	LISEVRLKQVAELAEILIGKNQYYETIQSFLQYVASEKRKLKVLKMERFAVGSMIASNIF
	EPLSQKKRLEVASLYYIKSFLCYIKNPYDELRRKADLHTIESAMKSAILSVQDVSGHDRT
	GDKFKKQDINNNEAPLSLVKFLQRMFEEDGYPNKEVESLERALKSNILKYQCSKFAYPTG
	TKDLVNADDKHKEEDQQDEKHADREQSTDLLEKTFVAHMVVESELLRSELFSQPKQRREN
	RSSGHELRKLPGKVAQSLQAVSFMDEHSIQTYVEIISLTKNNMAILNPLNENFDTKLSES
	SIATKLELRIEKILMAAGTIISPKNASDARVPGEQGKIIVLDAEDDSISELFYYKQTVNF
	SSDYRKLRKSIHTWETQSQFRQEQSLINRELVVVLITYIRALGFAKLQENDQDIRNSDME
	VLYDPTKLQVWVPTKKEWIHLKSQMEIVISITNEKTERRAQPQLVKEHLRPQQ
secondary structure: ''.join(['H' for i in range(1,90+1)])
sequence slice: "1-90"

#---assume an ideal coiled coil
oligomer specs:{'n_coils':2,'anti':True,'residue_shift':0}

residue_library: @martini/library-residues
sources: ['@martini/martini-sources.ff']
files: ['@martini/library-general-structs/martini-water.gro']
force field: martini-sources
review 3d: false
backwards script: @martini/bin/backward/backward.py
martinize script: @martini/bin/martinize.py
atomistic force field: charmm27

mdp specs:|{
    'group':'cgmd',
    'mdps':{
        'input-em-steep-in.mdp':['minimize'],
        },
    }

"""},

}