Sat Oct 8 11:52:08 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 Sat Oct 8 2011 at 11:52:09 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2492 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 190 has a net charge of 0.5140 !!! WARNING: HIR 196 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6367034 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): -24.59100 31.32200 ymin,ymax (A): -6.031000 40.33500 zmin,zma (A): 8.618000 50.86600 x,y,z range (A): 55.91300 46.36600 42.24800 scale (grids/A): 0.6367034 object centre (A): 3.365500 17.15200 29.74200 number of atom coordinates read : 2492 total number of charged atoms : 2352 net assigned charge : -1.957993 assigned positive charge : 383.7003 centred at (gu) : 89.95090 89.64941 90.84113 assigned negative charge : -385.6586 centred at (gu) : 90.06118 89.52080 90.84736 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6698 nv = 96 ne = 84 npr = 51055 no. pairs analyzed = 51055 no. exposed pairs = 2955 no. arc points = 21567 no. surface atoms = 1002 nbur = 1490 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3658 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3300000 number of dielectric boundary points 3353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2122 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8113 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5703765E-09 -3.7980019E-09 midg,1,midg; midg,igrid,midg -1.7628391E-08 1.0090765E-08 1,midg,midg; igrid,midg,midg 9.1138510E-09 -1.4186075E-08 gauss-seidel spectral radius is 0.9872105 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 11:52:09 rms-change max change #iterations 0.1462779 20.95725 at 10iterations 1.4441567E-02 2.088284 at 20iterations 1.3945916E-03 0.2230473 at 30iterations 1.3582743E-04 2.0393968E-02 at 40iterations 1.3233788E-05 1.8768311E-03 at 50iterations finished qdiffx linear iterations at : 11:52:13 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.3233788E-05 1.8768311E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 11:52:13 4.033u 0.260s 0:04.58 93.6% 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 Sat Oct 8 2011 at 11:52:13 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2492 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 190 has a net charge of 0.5140 !!! WARNING: HIR 196 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.910110 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): -24.59100 31.32200 ymin,ymax (A): -6.031000 40.33500 zmin,zma (A): 8.618000 50.86600 x,y,z range (A): 55.91300 46.36600 42.24800 scale (grids/A): 1.910110 object centre (A): 3.365500 17.15200 29.74200 number of atom coordinates read : 2492 total number of charged atoms : 2352 net assigned charge : -1.957993 assigned positive charge : 383.7003 centred at (gu) : 89.85263 88.94772 92.52313 assigned negative charge : -385.6586 centred at (gu) : 90.18333 88.56212 92.54205 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21567 grid for indexing accessible points = 1.400000 m= 24829 mr = 50484 m= 3779 mr = 18021 m= 275 mr = 2262 m= 2 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2461 time to turn everything in is 0.6400000 number of dielectric boundary points 30785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18488 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) : 0.6367034 object centre at (A) : 3.365500 17.15200 29.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7626182E-03 -1.4125990E-02 midg,1,midg; midg,igrid,midg -1.6140517E-02 2.7368201E-03 1,midg,midg; igrid,midg,midg 2.2990279E-02 -4.6866965E-02 gauss-seidel spectral radius is 0.9986327 estimated iterations to convergence 214 setup time was (sec) 0.9400000 now iterating at: 11:52:14 rms-change max change #iterations 4.238008 176.4761 at 10iterations 1.980744 69.31494 at 20iterations 0.9249833 35.80148 at 30iterations 0.4318590 13.83167 at 40iterations 0.2025993 6.527451 at 50iterations 9.4943218E-02 2.937030 at 60iterations 4.4193201E-02 1.403206 at 70iterations 2.0713024E-02 0.6645489 at 80iterations 9.7141145E-03 0.3074341 at 90iterations 4.5344681E-03 0.1429749 at 100iterations 2.1298840E-03 6.8666935E-02 at 110iterations 9.9578989E-04 3.1062603E-02 at 120iterations finished qdiffx linear iterations at : 11:52:23 total time elapsed so far: 9.110000 # loops : 120 mean,max change (kT/e) : 9.9578989E-04 3.1062603E-02 energy calculations done at 9.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.290000 DelPhi exited at 11:52:23 9.297u 0.280s 0:09.90 96.6% 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 Sat Oct 8 2011 at 11:52:23 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2492 !!! WARNING: HIR 186 has a net charge of 0.5140 !!! WARNING: HIR 190 has a net charge of 0.5140 !!! WARNING: HIR 196 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.865165 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): -24.59100 31.32200 ymin,ymax (A): -6.031000 40.33500 zmin,zma (A): 8.618000 50.86600 x,y,z range (A): 55.91300 46.36600 42.24800 scale (grids/A): 2.865165 object centre (A): 3.365500 17.15200 29.74200 number of atom coordinates read : 2492 total number of charged atoms : 2352 net assigned charge : -1.957993 assigned positive charge : 383.7003 centred at (gu) : 89.77876 88.42144 93.78490 assigned negative charge : -385.6586 centred at (gu) : 90.27496 87.84308 93.81297 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 168419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21567 grid for indexing accessible points = 1.400000 m= 81748 mr = 122470 m= 28271 mr = 66524 m= 6654 mr = 22233 m= 1148 mr = 4967 m= 79 mr = 768 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 8308 time to turn everything in is 1.610000 number of dielectric boundary points 69324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 18814 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) : 1.910110 object centre at (A) : 3.365500 17.15200 29.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6679145E-02 -0.2215460 midg,1,midg; midg,igrid,midg -0.1615897 -3.8784645E-02 1,midg,midg; igrid,midg,midg 0.2804838 -0.7443272 gauss-seidel spectral radius is 0.9992528 estimated iterations to convergence 289 setup time was (sec) 1.930000 now iterating at: 11:52:25 rms-change max change #iterations 9.863662 355.8199 at 10iterations 5.709822 125.4282 at 20iterations 3.289375 72.07286 at 30iterations 1.882593 34.71365 at 40iterations 1.079171 21.45228 at 50iterations 0.6187854 11.95401 at 60iterations 0.3546906 6.526349 at 70iterations 0.2028972 3.787815 at 80iterations 0.1164570 2.012726 at 90iterations 6.6359498E-02 1.247711 at 100iterations 3.8051054E-02 0.6996593 at 110iterations 2.1749955E-02 0.3955278 at 120iterations 1.2440401E-02 0.2130089 at 130iterations 7.1270023E-03 0.1396747 at 140iterations 4.0736441E-03 7.3974609E-02 at 150iterations 2.3313353E-03 4.3758392E-02 at 160iterations 1.3330425E-03 2.3178101E-02 at 170iterations 7.6123729E-04 1.4099121E-02 at 180iterations finished qdiffx linear iterations at : 11:52:39 total time elapsed so far: 15.26000 # loops : 180 mean,max change (kT/e) : 7.6123729E-04 1.4099121E-02 energy calculations done at 15.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.44000 DelPhi exited at 11:52:39 15.443u 0.306s 0:16.02 98.2% 0+0k 0+0io 0pf+0w