Sun Oct 9 16:02:16 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+sph2.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 = amb2.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 16:02:16 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5450 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5143765 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): 153.9750 218.2190 ymin,ymax (A): 94.70100 160.0410 zmin,zma (A): -1.401000 67.80900 x,y,z range (A): 64.24399 65.34000 69.21000 scale (grids/A): 0.5143765 object centre (A): 186.0970 127.3710 33.20400 number of atom coordinates read : 5450 total number of charged atoms : 5278 net assigned charge : 1.000033 assigned positive charge : 836.3768 centred at (gu) : 90.46355 88.23773 89.42989 assigned negative charge : -835.3839 centred at (gu) : 90.51141 88.27308 89.39523 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8900 nv = 96 ne = 84 npr = 110735 no. pairs analyzed = 110735 no. exposed pairs = 6338 no. arc points = 43811 no. surface atoms = 2118 nbur = 3332 mkacc time = 0.3000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 326 mr = 4875 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.5800000 number of dielectric boundary points 4341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4267 ## 606 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 12065 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2548497E-10 1.1898091E-10 midg,1,midg; midg,igrid,midg 2.2530046E-10 -6.9028540E-11 1,midg,midg; igrid,midg,midg 1.6329688E-10 -1.7545904E-10 gauss-seidel spectral radius is 0.9807067 estimated iterations to convergence 59 setup time was (sec) 0.8500000 now iterating at: 16:02:17 rms-change max change #iterations 7.4938372E-02 11.11740 at 10iterations 6.4440491E-03 0.9755173 at 20iterations 2.0154172E-03 0.3302898 at 30iterations 8.3555252E-04 0.1414986 at 40iterations 3.4712034E-04 5.9688568E-02 at 50iterations finished qdiffx linear iterations at : 16:02:20 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 3.4712034E-04 5.9688568E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 16:02:20 4.215u 0.280s 0:04.89 91.8% 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 16:02:21 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5450 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.543130 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): 153.9750 218.2190 ymin,ymax (A): 94.70100 160.0410 zmin,zma (A): -1.401000 67.80900 x,y,z range (A): 64.24399 65.34000 69.21000 scale (grids/A): 1.543130 object centre (A): 186.0970 127.3710 33.20400 number of atom coordinates read : 5450 total number of charged atoms : 5278 net assigned charge : 1.000033 assigned positive charge : 836.3768 centred at (gu) : 91.38896 84.71101 88.28767 assigned negative charge : -835.3839 centred at (gu) : 91.53392 84.81874 88.18530 start vw surface at 0.2400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 102693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43811 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30111 mr = 73207 m= 2645 mr = 20612 m= 58 mr = 1158 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3402 time to turn everything in is 0.8800000 number of dielectric boundary points 40531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 562 ## 9 charges are in solution ## iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 39715 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) : 0.5143765 object centre at (A) : 186.0970 127.3710 33.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0646548E-02 9.8587340E-04 midg,1,midg; midg,igrid,midg 2.2256164E-02 1.1508710E-03 1,midg,midg; igrid,midg,midg -2.0836281E-02 -1.5822424E-02 gauss-seidel spectral radius is 0.9981849 estimated iterations to convergence 186 setup time was (sec) 1.190000 now iterating at: 16:02:22 rms-change max change #iterations 4.208266 161.3904 at 10iterations 1.751651 55.11029 at 20iterations 0.7321190 20.95247 at 30iterations 0.3060127 9.027948 at 40iterations 0.1284963 3.579247 at 50iterations 5.4431856E-02 1.807018 at 60iterations 2.3458878E-02 0.7135372 at 70iterations 1.0696816E-02 0.3367310 at 80iterations 5.4594055E-03 0.1793213 at 90iterations 3.2681208E-03 0.1109276 at 100iterations 2.1970184E-03 7.6110840E-02 at 110iterations 1.5727889E-03 5.2482605E-02 at 120iterations finished qdiffx linear iterations at : 16:02:30 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 1.5727889E-03 5.2482605E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 16:02:31 9.553u 0.269s 0:10.39 94.4% 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 16:02:31 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5450 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.314694 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): 153.9750 218.2190 ymin,ymax (A): 94.70100 160.0410 zmin,zma (A): -1.401000 67.80900 x,y,z range (A): 64.24399 65.34000 69.21000 scale (grids/A): 2.314694 object centre (A): 186.0970 127.3710 33.20400 number of atom coordinates read : 5450 total number of charged atoms : 5278 net assigned charge : 1.000033 assigned positive charge : 836.3768 centred at (gu) : 92.08293 82.06602 87.43095 assigned negative charge : -835.3839 centred at (gu) : 92.30103 82.22811 87.27794 start vw surface at 0.2300000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 240414 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43811 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 108298 mr = 180051 m= 27476 mr = 86255 m= 3909 mr = 20193 m= 212 mr = 2391 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 11765 time to turn everything in is 2.140000 number of dielectric boundary points 91371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 42120 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) : 1.543130 object centre at (A) : 186.0970 127.3710 33.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5897287 0.2047048 midg,1,midg; midg,igrid,midg 0.4508382 -2.0375850E-02 1,midg,midg; igrid,midg,midg -0.4797571 -0.3555102 gauss-seidel spectral radius is 0.9991884 estimated iterations to convergence 277 setup time was (sec) 2.470000 now iterating at: 16:02:34 rms-change max change #iterations 11.24210 262.5087 at 10iterations 6.460242 169.1341 at 20iterations 3.698295 89.17719 at 30iterations 2.098791 46.98212 at 40iterations 1.189591 27.12813 at 50iterations 0.6731372 13.59912 at 60iterations 0.3797081 6.756870 at 70iterations 0.2136353 4.050247 at 80iterations 0.1202256 2.080686 at 90iterations 6.7597605E-02 1.231506 at 100iterations 3.8160108E-02 0.6093025 at 110iterations 2.1432349E-02 0.3940306 at 120iterations 1.2162283E-02 0.2184916 at 130iterations 6.9766119E-03 0.1291733 at 140iterations 4.0980461E-03 7.7934265E-02 at 150iterations 2.4944367E-03 4.9852371E-02 at 160iterations 1.6118585E-03 3.3451080E-02 at 170iterations 1.1165533E-03 2.2346497E-02 at 180iterations finished qdiffx linear iterations at : 16:02:48 total time elapsed so far: 16.28000 # loops : 180 mean,max change (kT/e) : 1.1165533E-03 2.2346497E-02 energy calculations done at 16.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.45000 DelPhi exited at 16:02:48 16.448u 0.313s 0:17.49 95.7% 0+0k 0+0io 0pf+0w