Sun Oct 9 00:43:36 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 00:43:36 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6530792 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -0.1920000 54.31900 ymin,ymax (A): -15.67300 27.65400 zmin,zma (A): 32.22300 83.84700 x,y,z range (A): 54.51100 43.32700 51.62400 scale (grids/A): 0.6530792 object centre (A): 27.06350 5.990501 58.03500 number of atom coordinates read : 2165 total number of charged atoms : 2032 net assigned charge : 11.50002 assigned positive charge : 316.3358 centred at (gu) : 90.54504 88.70369 88.84893 assigned negative charge : -304.8363 centred at (gu) : 90.57023 88.78671 88.87110 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6280 nv = 96 ne = 84 npr = 43263 no. pairs analyzed = 43263 no. exposed pairs = 2923 no. arc points = 20588 no. surface atoms = 972 nbur = 1193 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 3216 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.1700000 number of dielectric boundary points 3392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1994 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7380 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3956589E-08 1.6747164E-08 midg,1,midg; midg,igrid,midg 4.5304304E-08 1.0222761E-08 1,midg,midg; igrid,midg,midg 2.4349951E-08 2.3074902E-08 gauss-seidel spectral radius is 0.9878165 estimated iterations to convergence 74 setup time was (sec) 0.3600000 now iterating at: 00:43:37 rms-change max change #iterations 0.1396452 21.46325 at 10iterations 1.4257042E-02 2.421039 at 20iterations 1.5009205E-03 0.2426910 at 30iterations 1.5764736E-04 2.3708344E-02 at 40iterations 1.8177705E-05 2.8076172E-03 at 50iterations finished qdiffx linear iterations at : 00:43:40 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.8177705E-05 2.8076172E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 00:43:40 3.329u 0.176s 0:03.88 89.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 00:43:40 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.959238 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -0.1920000 54.31900 ymin,ymax (A): -15.67300 27.65400 zmin,zma (A): 32.22300 83.84700 x,y,z range (A): 54.51100 43.32700 51.62400 scale (grids/A): 1.959238 object centre (A): 27.06350 5.990501 58.03500 number of atom coordinates read : 2165 total number of charged atoms : 2032 net assigned charge : 11.50002 assigned positive charge : 316.3358 centred at (gu) : 91.63524 86.11116 86.54672 assigned negative charge : -304.8363 centred at (gu) : 91.71075 86.36036 86.61337 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20588 grid for indexing accessible points = 1.400000 m= 24352 mr = 44443 m= 4316 mr = 17347 m= 307 mr = 2599 m= 6 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1708 time to turn everything in is 0.3400000 number of dielectric boundary points 31273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 16034 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6530792 object centre at (A) : 27.06350 5.990501 58.03500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4969428E-02 3.7538897E-02 midg,1,midg; midg,igrid,midg 2.8845588E-02 -3.5749767E-03 1,midg,midg; igrid,midg,midg 7.0341952E-02 5.3479653E-02 gauss-seidel spectral radius is 0.9986691 estimated iterations to convergence 217 setup time was (sec) 0.5600000 now iterating at: 00:43:41 rms-change max change #iterations 3.947582 222.1923 at 10iterations 1.861007 66.91004 at 20iterations 0.8762196 31.13444 at 30iterations 0.4136980 14.82680 at 40iterations 0.1958832 6.793297 at 50iterations 9.1891751E-02 2.980577 at 60iterations 4.3539461E-02 1.457619 at 70iterations 2.0490604E-02 0.6459713 at 80iterations 9.6898582E-03 0.3113842 at 90iterations 4.5981626E-03 0.1524143 at 100iterations 2.1552292E-03 7.1132183E-02 at 110iterations 1.0235363E-03 3.1307220E-02 at 120iterations finished qdiffx linear iterations at : 00:43:48 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.0235363E-03 3.1307220E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 00:43:49 7.689u 0.190s 0:08.21 95.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 00:43:49 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2165 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.938856 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -0.1920000 54.31900 ymin,ymax (A): -15.67300 27.65400 zmin,zma (A): 32.22300 83.84700 x,y,z range (A): 54.51100 43.32700 51.62400 scale (grids/A): 2.938856 object centre (A): 27.06350 5.990501 58.03500 number of atom coordinates read : 2165 total number of charged atoms : 2032 net assigned charge : 11.50002 assigned positive charge : 316.3358 centred at (gu) : 92.45283 84.16671 84.81985 assigned negative charge : -304.8363 centred at (gu) : 92.56625 84.54050 84.91997 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 154233 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20588 grid for indexing accessible points = 1.400000 m= 77045 mr = 108271 m= 29377 mr = 61395 m= 7772 mr = 23061 m= 1304 mr = 5666 m= 115 mr = 837 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 5874 time to turn everything in is 0.8700000 number of dielectric boundary points 70543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 16256 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.959238 object centre at (A) : 27.06350 5.990501 58.03500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6040176 0.4894237 midg,1,midg; midg,igrid,midg 0.2555135 -2.7583234E-02 1,midg,midg; igrid,midg,midg 0.8650748 0.4821594 gauss-seidel spectral radius is 0.9992697 estimated iterations to convergence 292 setup time was (sec) 1.090000 now iterating at: 00:43:50 rms-change max change #iterations 9.323457 384.5475 at 10iterations 5.523519 150.5235 at 20iterations 3.249179 73.99062 at 30iterations 1.904318 42.55781 at 40iterations 1.112054 23.82643 at 50iterations 0.6467503 13.74240 at 60iterations 0.3767557 6.989120 at 70iterations 0.2186574 4.556670 at 80iterations 0.1264307 2.827942 at 90iterations 7.3348276E-02 1.461304 at 100iterations 4.2330962E-02 0.8440342 at 110iterations 2.4550663E-02 0.4655803 at 120iterations 1.4194711E-02 0.2897329 at 130iterations 8.1961472E-03 0.1527271 at 140iterations 4.7354517E-03 8.6961985E-02 at 150iterations 2.7335484E-03 5.3793371E-02 at 160iterations 1.5798453E-03 3.2627642E-02 at 170iterations 9.1284071E-04 1.8211365E-02 at 180iterations finished qdiffx linear iterations at : 00:44:01 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 9.1284071E-04 1.8211365E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 00:44:01 12.360u 0.228s 0:12.86 97.8% 0+0k 0+0io 0pf+0w