Mon Oct 10 18:36:11 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 Mon Oct 10 2011 at 18:36:11 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 = 2195 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6621531 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): -19.42300 34.34100 ymin,ymax (A): -6.992000 38.09800 zmin,zma (A): -2.668000 49.32200 x,y,z range (A): 53.76400 45.09000 51.99000 scale (grids/A): 0.6621531 object centre (A): 7.459000 15.55300 23.32700 number of atom coordinates read : 2195 total number of charged atoms : 2059 net assigned charge : 0.5000042 assigned positive charge : 322.5612 centred at (gu) : 92.33666 90.30419 90.98499 assigned negative charge : -322.0617 centred at (gu) : 92.28035 90.44182 91.11504 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6841 nv = 96 ne = 84 npr = 42865 no. pairs analyzed = 42865 no. exposed pairs = 2982 no. arc points = 21034 no. surface atoms = 996 nbur = 1199 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 3650 m= 7 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.1700000 number of dielectric boundary points 3601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1939 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7706 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9149656E-08 -2.6250150E-08 midg,1,midg; midg,igrid,midg 2.3270497E-08 -2.4116554E-08 1,midg,midg; igrid,midg,midg -5.0776032E-09 1.8258561E-08 gauss-seidel spectral radius is 0.9881549 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 18:36:12 rms-change max change #iterations 0.1512382 26.73513 at 10iterations 1.6377445E-02 2.545373 at 20iterations 1.7216271E-03 0.2672958 at 30iterations 2.0366166E-04 2.9083252E-02 at 40iterations 2.8400706E-05 4.8503876E-03 at 50iterations finished qdiffx linear iterations at : 18:36:15 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.8400706E-05 4.8503876E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 18:36:15 3.414u 0.188s 0:04.01 89.5% 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 Mon Oct 10 2011 at 18:36:15 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 = 2195 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.986459 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): -19.42300 34.34100 ymin,ymax (A): -6.992000 38.09800 zmin,zma (A): -2.668000 49.32200 x,y,z range (A): 53.76400 45.09000 51.99000 scale (grids/A): 1.986459 object centre (A): 7.459000 15.55300 23.32700 number of atom coordinates read : 2195 total number of charged atoms : 2059 net assigned charge : 0.5000042 assigned positive charge : 322.5612 centred at (gu) : 97.00947 90.91199 92.95449 assigned negative charge : -322.0617 centred at (gu) : 96.84095 91.32533 93.34504 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21034 grid for indexing accessible points = 1.400000 m= 29743 mr = 47771 m= 6274 mr = 22318 m= 481 mr = 4196 m= 4 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 0.3900000 number of dielectric boundary points 33240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16309 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) : 0.6621531 object centre at (A) : 7.459000 15.55300 23.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3311656E-02 7.4929837E-03 midg,1,midg; midg,igrid,midg 1.9042363E-02 -2.7612394E-03 1,midg,midg; igrid,midg,midg -8.6588915E-03 8.7515758E-03 gauss-seidel spectral radius is 0.9987157 estimated iterations to convergence 221 setup time was (sec) 0.6000000 now iterating at: 18:36:16 rms-change max change #iterations 4.146987 182.5506 at 10iterations 1.978637 72.51599 at 20iterations 0.9446609 28.80136 at 30iterations 0.4527854 14.49450 at 40iterations 0.2168134 6.798523 at 50iterations 0.1037446 3.409004 at 60iterations 4.9775131E-02 1.679161 at 70iterations 2.3935026E-02 0.7350292 at 80iterations 1.1447651E-02 0.3482351 at 90iterations 5.4798969E-03 0.1701660 at 100iterations 2.6418178E-03 8.1798553E-02 at 110iterations 1.2732017E-03 5.7067871E-02 at 120iterations finished qdiffx linear iterations at : 18:36:23 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.2732017E-03 5.7067871E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 18:36:24 7.903u 0.220s 0:08.60 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 Mon Oct 10 2011 at 18:36:24 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 = 2195 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.979689 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): -19.42300 34.34100 ymin,ymax (A): -6.992000 38.09800 zmin,zma (A): -2.668000 49.32200 x,y,z range (A): 53.76400 45.09000 51.99000 scale (grids/A): 2.979689 object centre (A): 7.459000 15.55300 23.32700 number of atom coordinates read : 2195 total number of charged atoms : 2059 net assigned charge : 0.5000042 assigned positive charge : 322.5612 centred at (gu) : 100.5141 91.36797 94.43151 assigned negative charge : -322.0617 centred at (gu) : 100.2614 91.98801 95.01753 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 163680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21034 grid for indexing accessible points = 1.400000 m= 88891 mr = 115517 m= 39666 mr = 72565 m= 11871 mr = 32681 m= 2107 mr = 9139 m= 145 mr = 1464 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 3362 time to turn everything in is 0.9900000 number of dielectric boundary points 74937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 16472 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) : 1.986459 object centre at (A) : 7.459000 15.55300 23.32700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7605601 0.3004866 midg,1,midg; midg,igrid,midg 0.1636428 8.9091919E-02 1,midg,midg; igrid,midg,midg 2.9963184E-02 0.2098339 gauss-seidel spectral radius is 0.9992776 estimated iterations to convergence 294 setup time was (sec) 1.210000 now iterating at: 18:36:25 rms-change max change #iterations 9.646020 369.3080 at 10iterations 5.685528 135.3799 at 20iterations 3.330054 74.55957 at 30iterations 1.945088 44.97768 at 40iterations 1.132861 22.00743 at 50iterations 0.6578290 12.40342 at 60iterations 0.3816201 7.034440 at 70iterations 0.2214195 4.557984 at 80iterations 0.1286465 2.435518 at 90iterations 7.4478261E-02 1.383911 at 100iterations 4.3096267E-02 0.8967419 at 110iterations 2.4926983E-02 0.4235573 at 120iterations 1.4443371E-02 0.2637997 at 130iterations 8.3352616E-03 0.1582966 at 140iterations 4.8422231E-03 8.8578224E-02 at 150iterations 2.7928406E-03 5.3699493E-02 at 160iterations 1.6203426E-03 2.8903246E-02 at 170iterations 9.3731692E-04 1.8688202E-02 at 180iterations finished qdiffx linear iterations at : 18:36:37 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 9.3731692E-04 1.8688202E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 18:36:37 12.744u 0.221s 0:13.40 96.7% 0+0k 0+0io 0pf+0w