Sun Oct 9 22:58:23 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 Sun Oct 9 2011 at 22:58:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4379 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: 0.5115750 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): -20.87700 31.22000 ymin,ymax (A): -30.39800 39.19100 zmin,zma (A): -64.29900 -0.2050000 x,y,z range (A): 52.09700 69.58900 64.09399 scale (grids/A): 0.5115750 object centre (A): 5.171501 4.396502 -32.25200 number of atom coordinates read : 4379 total number of charged atoms : 4219 net assigned charge : 4.000007 assigned positive charge : 662.8226 centred at (gu) : 89.30464 89.34695 91.67904 assigned negative charge : -658.8271 centred at (gu) : 89.44697 89.28071 91.76304 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7383 nv = 96 ne = 84 npr = 85416 no. pairs analyzed = 85416 no. exposed pairs = 5981 no. arc points = 41954 no. surface atoms = 1995 nbur = 2384 mkacc time = 0.1600000 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 = 1.708000 m= 257 mr = 3582 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4114 ## 642 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9978 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7267933E-10 -2.3659727E-10 midg,1,midg; midg,igrid,midg -1.2464656E-10 1.8933523E-10 1,midg,midg; igrid,midg,midg 4.9170740E-10 -2.4757230E-10 gauss-seidel spectral radius is 0.9804420 estimated iterations to convergence 59 setup time was (sec) 0.4800000 now iterating at: 22:58:24 rms-change max change #iterations 6.4228825E-02 10.65144 at 10iterations 3.5511150E-03 0.5249634 at 20iterations 2.8416992E-04 5.9135437E-02 at 30iterations 6.8298548E-05 1.7526627E-02 at 40iterations 2.2681887E-05 5.8979988E-03 at 50iterations finished qdiffx linear iterations at : 22:58:27 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 2.2681887E-05 5.8979988E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 22:58:27 3.551u 0.179s 0:04.02 92.5% 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 Sun Oct 9 2011 at 22:58:27 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 = 4379 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: 1.534725 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): -20.87700 31.22000 ymin,ymax (A): -30.39800 39.19100 zmin,zma (A): -64.29900 -0.2050000 x,y,z range (A): 52.09700 69.58900 64.09399 scale (grids/A): 1.534725 object centre (A): 5.171501 4.396502 -32.25200 number of atom coordinates read : 4379 total number of charged atoms : 4219 net assigned charge : 4.000007 assigned positive charge : 662.8226 centred at (gu) : 87.91203 88.03919 95.03550 assigned negative charge : -658.8271 centred at (gu) : 88.34052 87.84165 95.28886 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 83666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41954 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 23310 mr = 55357 m= 1888 mr = 15049 m= 44 mr = 719 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 266 time to turn everything in is 0.4200000 number of dielectric boundary points 37783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 594 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 31697 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) : 0.5115750 object centre at (A) : 5.171501 4.396502 -32.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7199520E-03 8.4311664E-03 midg,1,midg; midg,igrid,midg 1.6488840E-03 2.5251608E-02 1,midg,midg; igrid,midg,midg 1.4833411E-03 -1.0300954E-02 gauss-seidel spectral radius is 0.9980981 estimated iterations to convergence 182 setup time was (sec) 0.6400000 now iterating at: 22:58:28 rms-change max change #iterations 3.589210 159.1687 at 10iterations 1.461173 62.68654 at 20iterations 0.5956318 22.26122 at 30iterations 0.2427437 8.458672 at 40iterations 9.8466441E-02 3.261510 at 50iterations 4.0440496E-02 1.441063 at 60iterations 1.6447823E-02 0.5237007 at 70iterations 6.7418208E-03 0.2200928 at 80iterations 2.7642725E-03 9.0061665E-02 at 90iterations 1.1436067E-03 3.8112640E-02 at 100iterations 4.8388352E-04 1.7089844E-02 at 110iterations 2.1523103E-04 9.5825195E-03 at 120iterations finished qdiffx linear iterations at : 22:58:35 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 2.1523103E-04 9.5825195E-03 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 22:58:36 7.993u 0.208s 0:08.61 95.1% 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 22:58:36 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 = 4379 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: 2.302088 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): -20.87700 31.22000 ymin,ymax (A): -30.39800 39.19100 zmin,zma (A): -64.29900 -0.2050000 x,y,z range (A): 52.09700 69.58900 64.09399 scale (grids/A): 2.302088 object centre (A): 5.171501 4.396502 -32.25200 number of atom coordinates read : 4379 total number of charged atoms : 4219 net assigned charge : 4.000007 assigned positive charge : 662.8226 centred at (gu) : 86.86763 87.05839 97.55289 assigned negative charge : -658.8271 centred at (gu) : 87.51065 86.76227 97.93305 start vw surface at 0.1300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 194822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41954 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 84364 mr = 136561 m= 20389 mr = 64798 m= 2721 mr = 14234 m= 144 mr = 1501 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 862 time to turn everything in is 1.000000 number of dielectric boundary points 85305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 33654 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) : 1.534725 object centre at (A) : 5.171501 4.396502 -32.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1627208 0.2543664 midg,1,midg; midg,igrid,midg 6.8874195E-02 0.6571679 1,midg,midg; igrid,midg,midg -5.9551154E-03 -0.1533243 gauss-seidel spectral radius is 0.9991556 estimated iterations to convergence 272 setup time was (sec) 1.240000 now iterating at: 22:58:37 rms-change max change #iterations 9.917484 285.5515 at 10iterations 5.743021 152.1407 at 20iterations 3.269059 73.98671 at 30iterations 1.851302 45.66930 at 40iterations 1.041216 21.77736 at 50iterations 0.5841944 12.35298 at 60iterations 0.3270646 7.529919 at 70iterations 0.1826865 3.643150 at 80iterations 0.1017568 1.989483 at 90iterations 5.6548167E-02 1.135183 at 100iterations 3.1496692E-02 0.6266060 at 110iterations 1.7468920E-02 0.3331852 at 120iterations 9.6954042E-03 0.1835508 at 130iterations 5.3842100E-03 0.1080704 at 140iterations 2.9831084E-03 5.4309845E-02 at 150iterations 1.6537250E-03 3.1890869E-02 at 160iterations 9.1975287E-04 1.7883301E-02 at 170iterations 5.1005936E-04 9.0179443E-03 at 180iterations finished qdiffx linear iterations at : 22:58:49 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 5.1005936E-04 9.0179443E-03 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 22:58:49 12.932u 0.186s 0:13.43 97.6% 0+0k 0+0io 0pf+0w