Index

Symbols | A | C | E | O | P | S

Symbols

-am1bcc
szybki command line option
-calc <run_type>
command line option
-complex <filename>
szybki command line option
-current_charges
szybki command line option
-ensemble
command line option
-entropy <type>
szybki command line option
-ewindow
command line option
-exact_vdw
szybki command line option
-ff
szybki command line option
-ff <type>
command line option
-fix_file <filename>
szybki command line option
-fix_smarts <file_name>
szybki command line option
-flex_file <filename>
szybki command line option
-flexdist <d>
szybki command line option
-flexlist <fn>
szybki command line option
-flextype <type>
szybki command line option
-grad_conv <c>
szybki command line option
-harm_constr1 <k>
szybki command line option
-harm_constr2 <d>
szybki command line option
-harm_smarts <file.txt>
szybki command line option
-heavy_rms
szybki command line option
-i <filename>
command line option
szybki command line option
-in <filename>
command line option
szybki command line option
-inner_dielectric <d>
szybki command line option
-ionic <type>
command line option
-keepFailures
szybki command line option
-l <filename>
szybki command line option
-largest_part
szybki command line option
-ligands <filename>
szybki command line option
-loadPG <filename>
szybki command line option
-log <prefix>
szybki command line option
-max_iter <m>
szybki command line option
-maxconfs <value>
command line option
-MMFF94S
szybki command line option
-mod_vdw
szybki command line option
-mpi_hostfile <filename>
szybki command line option
-mpi_np <n>
szybki command line option
-neglect_frozen
szybki command line option
-noCoulomb
szybki command line option
-o <filename>
szybki command line option
-optDOF
szybki command line option
-optdof
szybki command line option
-optGeometry <dof>
szybki command line option
-optMethod <type>
szybki command line option
-out <filename>
command line option
szybki command line option
-out_complex <filename>
szybki command line option
-out_protein <filename>
szybki command line option
-p <filename>
szybki command line option
-param
szybki command line option
-param <filename>
command line option
-PBsolvent_dielectric <value>
command line option
-polarH <r>
szybki command line option
-prefix <p>
command line option
-prefix <pn>
szybki command line option
-protein <filename>
szybki command line option
-protein_elec <m>
szybki command line option
-protein_vdw <r>
szybki command line option
-radii <type>
szybki command line option
-report
szybki command line option
-report <filename>
command line option
-reportFile <filename>
szybki command line option
-residue <r>
szybki command line option
-rms <value>
command line option
-rws
szybki command line option
-salt <c>
szybki command line option
-savePG <filename>
szybki command line option
-sdtag <string>
szybki command line option
-sfp
szybki command line option
-shefA <a>
szybki command line option
-shefB <b>
szybki command line option
-sheffield
szybki command line option
-sideC <r>
szybki command line option
-silent
szybki command line option
-solv_dielectric <d>
szybki command line option
-solvcharges <type>
command line option
-solvent <type>
command line option
-solventCA <s>
szybki command line option
-solventPB
szybki command line option
-strict
szybki command line option
-strip_water
szybki command line option
-t
szybki command line option
-tor_constr <fn>
szybki command line option
-track <filename>
command line option
-vdw_cutoff
szybki command line option
-verbose
szybki command line option

A

APPNAME_OE_ARCH

C

command line option
-PBsolvent_dielectric <value>
-calc <run_type>
-ensemble
-ewindow
-ff <type>
-i <filename>
-in <filename>
-ionic <type>
-maxconfs <value>
-out <filename>
-param <filename>
-prefix <p>
-report <filename>
-rms <value>
-solvcharges <type>
-solvent <type>
-track <filename>

E

environment variable
APPNAME_OE_ARCH
OE_ARCH, [1], [2], [3]
OE_LICENSE
PATH, [1], [2], [3], [4]

O

OE_ARCH, [1], [2], [3]
OE_LICENSE

P

PATH, [1], [2], [3], [4]

S

szybki command line option
-MMFF94S
-am1bcc
-complex <filename>
-current_charges
-entropy <type>
-exact_vdw
-ff
-fix_file <filename>
-fix_smarts <file_name>
-flex_file <filename>
-flexdist <d>
-flexlist <fn>
-flextype <type>
-grad_conv <c>
-harm_constr1 <k>
-harm_constr2 <d>
-harm_smarts <file.txt>
-heavy_rms
-i <filename>
-in <filename>
-inner_dielectric <d>
-keepFailures
-l <filename>
-largest_part
-ligands <filename>
-loadPG <filename>
-log <prefix>
-max_iter <m>
-mod_vdw
-mpi_hostfile <filename>
-mpi_np <n>
-neglect_frozen
-noCoulomb
-o <filename>
-optDOF
-optGeometry <dof>
-optMethod <type>
-optdof
-out <filename>
-out_complex <filename>
-out_protein <filename>
-p <filename>
-param
-polarH <r>
-prefix <pn>
-protein <filename>
-protein_elec <m>
-protein_vdw <r>
-radii <type>
-report
-reportFile <filename>
-residue <r>
-rws
-salt <c>
-savePG <filename>
-sdtag <string>
-sfp
-shefA <a>
-shefB <b>
-sheffield
-sideC <r>
-silent
-solv_dielectric <d>
-solventCA <s>
-solventPB
-strict
-strip_water
-t
-tor_constr <fn>
-vdw_cutoff
-verbose