surf
Calculate the LCPO surface area of specified atoms. Can do partial surface areas.
surf [<name>] [<mask1>] [out <filename>] [solutemask <mask>] [offset <offset>] [nbrcut <cut>]
<name> Output data set name.
<mask1> Atoms to calculate surface area for.
out <filename> File to write surface area to.
solutemask <mask> If specified, calculate the contribution of <mask1> to <mask>.
offset <offset> Increment van der Waals radii by <offset>; 1.4 Ang. is the default (as used by Amber).
nbrcut <cut> Only atoms with van der Waals radii greater than <cut> are considered to have neighbors (2.5 Ang Amber default).
Calculate the surface area in 
Note that even if <mask> does not include all solute atoms, the neighbor list is still calculated for all solute atoms so the surface area calculated reflects the contribution of atoms in <mask> to the overall surface area, not the surface area of <mask> as an isolated system. As a result, it may be possible to obtain a negative surface area
if only a small fraction of the solute is selected.
For example, to calculate the overall surface area of all solute atoms, as well as the contribution of residue 1 to the overall surface area, writing both results to surf.dat:
surf out surf.dat surf :1 out surf.dat
Another example:
########################################## noexitonerror parm nowater.topo trajin 1/nowater.nc 1 last 1 trajin 2/nowater.nc 1 last 1 trajin 3/nowater.nc 1 last 1 trajin 4/nowater.nc 1 last 1 trajin 5/nowater.nc 1 last 1 check @N1,N2,P,OP1,OP2,C1',C2',C3',C4',O3',O4' skipbadframes silent ########################################## rms r1 :1-$last_resid mass out data/rms_all.dat time 20 hist r1 norm min 0 max 20 bins 200 out data/rms_all.hist atomicfluct out data/fluct_byatom_bfactor.dat :1-$last_resid bfactor atomicfluct out data/fluct_byres_bfactor.dat :1-32 byres bfactor distance e1 out data/end-to-end-bp1.dat :1,$first_resid :$firstresidplusone,$last_resid time 20 surf s1 :1-$last_resid out data/surf.dat run runanalysis avg s1 out data/surf-avg.dat pwd go