Energy parameter

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parameter is a second level energy command used to specify the solvent model, force field and various other energy terms.

Contents

[edit] General Energy Parameters

badcont[act] - bad contact term
pipack[ing] - pi-packing term
hbcalc - hydrogen bonding calculation
selfcont[act] - 
adjust
angle_scale
con[tact]
csurf_grid_reso
ff - specify the force field, see force field for the complete list
hbb
ignore_frz_energy
ionic
np - non-polar options
npparam - non-polar parameters
npsurf - non-polar surface
packing
pena[lty] - sgb penalty
pH
screen2_cutoff
screen2_width
screen_cutoff
screen_width
sgbcut_low
sgbcut_med
sgbscale
solv[ent] - set the solvent to use, see solvent for the complete list
stacking
surf_grid1
surf_grid2
torsion_scale
twobond
use_bci - use bond charge increment list, this becomes very memory intensive for larger structures, and is probably not recommended
use_sgbfrz_zip
use_zipped_pair
vdw_restore
vdw_scale
rbuffer
watermap

[edit] Energy Weighting Parameters

wtenergy - ?
wt14el - 1-4 electrostatic weight
wt14lj - 1-4 lennard-jones weight
wtangl - 1-4 angle weight
wtbond - covalent bond weight
wtel - electrostatic weight
wtlj - lennard-jones weight
wttor - torsion weight

[edit] Distance Cutoffs

nbcut1_cc - nonbonded distance cut
nbcut1_cn - nonbonded distance cut
nbcut1_nn - nonbonded distance cut
nbcut2_cc - nonbonded distance cut
nbcut2_cn - nonbonded distance cut
nbcut2_nn - nonbonded distance cut

[edit] Dielectric Screening Constants

diel_ext - exterior dielectric (80 for water, default)
diel_int - interior dielectric (1 for protein, default)
var_diel - enable variable dielectric
arg_diel - set dielectric for arginine
asp_diel - set dielectric for asparagine
glu_diel - set dielectric for glutamine
hip_diel - 
his_diel - set dielectric for 
lys_diel - set dielectric for lysine
vd_lig - variable dielectric of the ligand
vd_pro - variable dielectric of the protein

[edit] Lipophilic Term Parameters

lipocoef_ca
lipocoef_cm
lipocoef_cn
lipocoef_ct
lipocoef_cz
lipocoeff
lipocoef_s
liposym
lipotypebased
uselipo
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