Mon Oct 10 22:34:13 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 22:34:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6178839 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): 17.62600 75.24200 ymin,ymax (A): -11.14900 43.18200 zmin,zma (A): -8.477000 34.94900 x,y,z range (A): 57.61600 54.33100 43.42600 scale (grids/A): 0.6178839 object centre (A): 46.43400 16.01650 13.23600 number of atom coordinates read : 2625 total number of charged atoms : 2484 net assigned charge : 5.500018 assigned positive charge : 394.2678 centred at (gu) : 88.41930 89.98702 89.95416 assigned negative charge : -388.7685 centred at (gu) : 88.71181 90.10625 90.13219 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6563 nv = 96 ne = 84 npr = 53738 no. pairs analyzed = 53738 no. exposed pairs = 3023 no. arc points = 21085 no. surface atoms = 1026 nbur = 1599 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3723 m= 0 mr = 31 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3200000 number of dielectric boundary points 3097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2085 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8089 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4915692E-08 -7.4241555E-09 midg,1,midg; midg,igrid,midg 1.1242036E-08 -3.6907182E-09 1,midg,midg; igrid,midg,midg 3.0756244E-08 -1.0516293E-08 gauss-seidel spectral radius is 0.9864331 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 22:34:14 rms-change max change #iterations 0.1254157 17.84551 at 10iterations 1.1997601E-02 1.907028 at 20iterations 1.6352271E-03 0.3066101 at 30iterations 3.8807385E-04 9.0126038E-02 at 40iterations 1.1236255E-04 2.7095795E-02 at 50iterations finished qdiffx linear iterations at : 22:34:16 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.1236255E-04 2.7095795E-02 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 22:34:17 3.110u 0.138s 0:03.77 85.9% 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 Mon Oct 10 2011 at 22:34:17 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 = 2625 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: 1.853652 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): 17.62600 75.24200 ymin,ymax (A): -11.14900 43.18200 zmin,zma (A): -8.477000 34.94900 x,y,z range (A): 57.61600 54.33100 43.42600 scale (grids/A): 1.853652 object centre (A): 46.43400 16.01650 13.23600 number of atom coordinates read : 2625 total number of charged atoms : 2484 net assigned charge : 5.500018 assigned positive charge : 394.2678 centred at (gu) : 85.25728 89.96045 89.86202 assigned negative charge : -388.7685 centred at (gu) : 86.13539 90.31834 90.39645 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 71665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21085 grid for indexing accessible points = 1.400000 m= 24688 mr = 50760 m= 3534 mr = 18517 m= 150 mr = 2254 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2818 time to turn everything in is 0.5700000 number of dielectric boundary points 28472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19454 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) : 0.6178839 object centre at (A) : 46.43400 16.01650 13.23600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8787961E-02 1.4157876E-03 midg,1,midg; midg,igrid,midg 3.5719402E-02 8.2122181E-03 1,midg,midg; igrid,midg,midg 4.3031503E-03 -5.4811284E-02 gauss-seidel spectral radius is 0.9985568 estimated iterations to convergence 209 setup time was (sec) 0.8600000 now iterating at: 22:34:18 rms-change max change #iterations 4.036546 154.9802 at 10iterations 1.840063 66.93298 at 20iterations 0.8427117 26.63612 at 30iterations 0.3865731 13.75886 at 40iterations 0.1778177 5.563355 at 50iterations 8.1704780E-02 2.557836 at 60iterations 3.7668355E-02 1.199638 at 70iterations 1.7346308E-02 0.5668199 at 80iterations 8.1141917E-03 0.2553864 at 90iterations 3.8943223E-03 0.1479111 at 100iterations 1.9144492E-03 7.1920395E-02 at 110iterations 1.0040024E-03 4.1465759E-02 at 120iterations finished qdiffx linear iterations at : 22:34:24 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 1.0040024E-03 4.1465759E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 22:34:24 6.947u 0.162s 0:07.60 93.4% 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 22:34:24 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 = 2625 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.780478 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): 17.62600 75.24200 ymin,ymax (A): -11.14900 43.18200 zmin,zma (A): -8.477000 34.94900 x,y,z range (A): 57.61600 54.33100 43.42600 scale (grids/A): 2.780478 object centre (A): 46.43400 16.01650 13.23600 number of atom coordinates read : 2625 total number of charged atoms : 2484 net assigned charge : 5.500018 assigned positive charge : 394.2678 centred at (gu) : 82.88577 89.94058 89.79286 assigned negative charge : -388.7685 centred at (gu) : 84.20300 90.47743 90.59458 start vw surface at 0.2200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 166246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21085 grid for indexing accessible points = 1.400000 m= 82042 mr = 122845 m= 28000 mr = 67995 m= 6372 mr = 22923 m= 738 mr = 4929 m= 17 mr = 487 m= 0 mr = 4 time to grow re-entrant surface = 0.6900000 no. cavity mid-points inaccessible to solvent = 9678 time to turn everything in is 1.270000 number of dielectric boundary points 64232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 19872 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) : 1.853652 object centre at (A) : 46.43400 16.01650 13.23600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2887555 4.4651501E-02 midg,1,midg; midg,igrid,midg 0.4173173 0.1514768 1,midg,midg; igrid,midg,midg -0.1019082 -0.7182713 gauss-seidel spectral radius is 0.9992338 estimated iterations to convergence 285 setup time was (sec) 1.550000 now iterating at: 22:34:26 rms-change max change #iterations 9.501766 384.9247 at 10iterations 5.448186 114.1196 at 20iterations 3.111269 76.88283 at 30iterations 1.771632 36.03643 at 40iterations 1.010149 20.02687 at 50iterations 0.5759076 10.51112 at 60iterations 0.3279265 6.571676 at 70iterations 0.1864409 3.622177 at 80iterations 0.1062459 2.067596 at 90iterations 6.0459845E-02 1.159456 at 100iterations 3.4380693E-02 0.6416302 at 110iterations 1.9624559E-02 0.3983917 at 120iterations 1.1249783E-02 0.2182121 at 130iterations 6.5049143E-03 0.1480408 at 140iterations 3.7852277E-03 8.1541061E-02 at 150iterations 2.2615336E-03 5.3764343E-02 at 160iterations 1.3976867E-03 3.2924652E-02 at 170iterations 9.0995460E-04 2.2846222E-02 at 180iterations finished qdiffx linear iterations at : 22:34:35 total time elapsed so far: 10.82000 # loops : 180 mean,max change (kT/e) : 9.0995460E-04 2.2846222E-02 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 22:34:36 10.984u 0.206s 0:11.53 96.9% 0+0k 0+0io 0pf+0w