Mon Oct 10 14:25:17 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 Mon Oct 10 2011 at 14:25:17 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5909891 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 0.5909891 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 389.9810 centred at (gu) : 90.00133 90.83223 89.57375 assigned negative charge : -389.9814 centred at (gu) : 89.82736 90.67789 89.63328 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6047 nv = 96 ne = 84 npr = 52695 no. pairs analyzed = 52695 no. exposed pairs = 3509 no. arc points = 24880 no. surface atoms = 1186 nbur = 1436 mkacc time = 0.1200000 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 = 1.456000 m= 272 mr = 3039 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2425 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7538 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7617453E-09 -1.5339382E-09 midg,1,midg; midg,igrid,midg -3.6064027E-09 5.0456492E-09 1,midg,midg; igrid,midg,midg -4.9417284E-09 4.6706945E-09 gauss-seidel spectral radius is 0.9851912 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 14:25:17 rms-change max change #iterations 0.1018622 16.91826 at 10iterations 8.2745776E-03 1.182549 at 20iterations 6.7919615E-04 0.1211700 at 30iterations 5.5191249E-05 1.0393143E-02 at 40iterations 4.6378018E-06 7.4958801E-04 at 50iterations finished qdiffx linear iterations at : 14:25:20 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 4.6378018E-06 7.4958801E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 14:25:21 3.529u 0.185s 0:04.04 91.5% 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 14:25:21 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.772967 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 1.772967 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 389.9810 centred at (gu) : 90.00336 92.49651 88.72097 assigned negative charge : -389.9814 centred at (gu) : 89.48181 92.03320 88.89947 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 66195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24880 grid for indexing accessible points = 1.400000 m= 20873 mr = 44153 m= 2281 mr = 13932 m= 111 mr = 987 m= 0 mr = 20 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19251 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) : 0.5909891 object centre at (A) : 18.24750 43.24300 81.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8128446E-03 1.5282714E-03 midg,1,midg; midg,igrid,midg -5.2663852E-03 1.2136688E-02 1,midg,midg; igrid,midg,midg -2.3484329E-02 6.0517234E-03 gauss-seidel spectral radius is 0.9984345 estimated iterations to convergence 201 setup time was (sec) 0.8300000 now iterating at: 14:25:22 rms-change max change #iterations 3.709296 174.3349 at 10iterations 1.629557 59.92798 at 20iterations 0.7252313 25.60572 at 30iterations 0.3201829 11.77835 at 40iterations 0.1415212 5.095196 at 50iterations 6.2975973E-02 2.372778 at 60iterations 2.7947102E-02 0.9185364 at 70iterations 1.2365610E-02 0.4062052 at 80iterations 5.4954765E-03 0.2014589 at 90iterations 2.4372209E-03 9.5859528E-02 at 100iterations 1.0840337E-03 3.9784908E-02 at 110iterations 4.8126903E-04 1.6687393E-02 at 120iterations finished qdiffx linear iterations at : 14:25:29 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 4.8126903E-04 1.6687393E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 14:25:29 7.914u 0.210s 0:08.41 96.5% 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 14:25:29 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 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: 2.659451 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): -7.579000 44.07400 ymin,ymax (A): 13.12400 73.36200 zmin,zma (A): 55.66800 106.7240 x,y,z range (A): 51.65300 60.23800 51.05600 scale (grids/A): 2.659451 object centre (A): 18.24750 43.24300 81.19600 number of atom coordinates read : 2622 total number of charged atoms : 2475 net assigned charge : 5.1110983E-06 assigned positive charge : 389.9810 centred at (gu) : 90.00510 93.74447 88.08142 assigned negative charge : -389.9814 centred at (gu) : 89.22259 93.04980 88.34914 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 153237 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24880 grid for indexing accessible points = 1.400000 m= 70781 mr = 107784 m= 21007 mr = 55240 m= 3383 mr = 15165 m= 312 mr = 2039 m= 12 mr = 137 m= 0 mr = 6 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 68361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 19794 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) : 1.772967 object centre at (A) : 18.24750 43.24300 81.19600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2004567 2.3156971E-02 midg,1,midg; midg,igrid,midg -5.1832676E-02 3.3938989E-02 1,midg,midg; igrid,midg,midg -0.3030455 2.9701572E-02 gauss-seidel spectral radius is 0.9992114 estimated iterations to convergence 281 setup time was (sec) 1.570000 now iterating at: 14:25:31 rms-change max change #iterations 9.206736 316.9040 at 10iterations 5.367163 132.3242 at 20iterations 3.079920 74.94440 at 30iterations 1.761853 40.82366 at 40iterations 1.007518 21.80406 at 50iterations 0.5738004 12.92308 at 60iterations 0.3246924 7.822639 at 70iterations 0.1843072 3.978958 at 80iterations 0.1042607 2.300117 at 90iterations 5.9091460E-02 1.267228 at 100iterations 3.3431008E-02 0.6953888 at 110iterations 1.8890070E-02 0.3704586 at 120iterations 1.0672433E-02 0.2257442 at 130iterations 6.0289493E-03 0.1172776 at 140iterations 3.4025477E-03 7.1923733E-02 at 150iterations 1.9192779E-03 3.9767265E-02 at 160iterations 1.0836050E-03 2.0782471E-02 at 170iterations 6.1095314E-04 1.1345863E-02 at 180iterations finished qdiffx linear iterations at : 14:25:42 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 6.1095314E-04 1.1345863E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 14:25:43 12.713u 0.218s 0:13.26 97.4% 0+0k 0+0io 0pf+0w