Sun Oct 9 10:33:22 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 10:33:22 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 = 2217 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6408641 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): -1.583000 47.91000 ymin,ymax (A): -24.34000 31.21000 zmin,zma (A): -5.379000 47.44100 x,y,z range (A): 49.49300 55.55000 52.82000 scale (grids/A): 0.6408641 object centre (A): 23.16350 3.435000 21.03100 number of atom coordinates read : 2217 total number of charged atoms : 2080 net assigned charge : 1.500014 assigned positive charge : 322.3855 centred at (gu) : 90.69334 90.12904 91.12712 assigned negative charge : -320.8863 centred at (gu) : 90.69551 89.95043 91.08637 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6275 nv = 96 ne = 84 npr = 44208 no. pairs analyzed = 44208 no. exposed pairs = 3025 no. arc points = 21162 no. surface atoms = 1021 nbur = 1196 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3240 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1700000 number of dielectric boundary points 3345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2067 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7317 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4325358E-09 7.8747693E-09 midg,1,midg; midg,igrid,midg -1.5342136E-08 2.0004521E-08 1,midg,midg; igrid,midg,midg 2.0728372E-09 2.2646263E-09 gauss-seidel spectral radius is 0.9873611 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 10:33:23 rms-change max change #iterations 0.1304828 21.29662 at 10iterations 1.2805887E-02 2.274632 at 20iterations 1.2348611E-03 0.1829300 at 30iterations 1.2332390E-04 1.8927574E-02 at 40iterations 1.2336358E-05 1.8558502E-03 at 50iterations finished qdiffx linear iterations at : 10:33:26 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.2336358E-05 1.8558502E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 10:33:26 3.354u 0.177s 0:03.83 91.9% 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 Sun Oct 9 2011 at 10:33:26 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 = 2217 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: 1.922592 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): -1.583000 47.91000 ymin,ymax (A): -24.34000 31.21000 zmin,zma (A): -5.379000 47.44100 x,y,z range (A): 49.49300 55.55000 52.82000 scale (grids/A): 1.922592 object centre (A): 23.16350 3.435000 21.03100 number of atom coordinates read : 2217 total number of charged atoms : 2080 net assigned charge : 1.500014 assigned positive charge : 322.3855 centred at (gu) : 92.07990 90.38671 93.38126 assigned negative charge : -320.8863 centred at (gu) : 92.08681 89.85133 93.25922 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66990 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21162 grid for indexing accessible points = 1.400000 m= 23691 mr = 44353 m= 4138 mr = 17087 m= 318 mr = 2674 m= 4 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 0.3500000 number of dielectric boundary points 30909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 16384 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) : 0.6408641 object centre at (A) : 23.16350 3.435000 21.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4114008E-02 3.8281143E-02 midg,1,midg; midg,igrid,midg -1.7579006E-02 2.4495047E-02 1,midg,midg; igrid,midg,midg -1.2815283E-02 -1.8510217E-02 gauss-seidel spectral radius is 0.9986314 estimated iterations to convergence 214 setup time was (sec) 0.5700000 now iterating at: 10:33:27 rms-change max change #iterations 3.857317 168.6246 at 10iterations 1.795954 73.17291 at 20iterations 0.8405340 27.72375 at 30iterations 0.3945748 13.43359 at 40iterations 0.1837236 6.256035 at 50iterations 8.5911401E-02 2.913654 at 60iterations 4.0014781E-02 1.340881 at 70iterations 1.8742975E-02 0.5868874 at 80iterations 8.7596821E-03 0.2877941 at 90iterations 4.1086655E-03 0.1344795 at 100iterations 1.9133386E-03 6.4771652E-02 at 110iterations 8.9801900E-04 3.0652761E-02 at 120iterations finished qdiffx linear iterations at : 10:33:34 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 8.9801900E-04 3.0652761E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 10:33:35 7.873u 0.196s 0:08.36 96.4% 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 Sun Oct 9 2011 at 10:33:35 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 = 2217 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.883888 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): -1.583000 47.91000 ymin,ymax (A): -24.34000 31.21000 zmin,zma (A): -5.379000 47.44100 x,y,z range (A): 49.49300 55.55000 52.82000 scale (grids/A): 2.883888 object centre (A): 23.16350 3.435000 21.03100 number of atom coordinates read : 2217 total number of charged atoms : 2080 net assigned charge : 1.500014 assigned positive charge : 322.3855 centred at (gu) : 93.11974 90.57996 95.07166 assigned negative charge : -320.8863 centred at (gu) : 93.13030 89.77693 94.88880 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 154875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21162 grid for indexing accessible points = 1.400000 m= 75302 mr = 108411 m= 28507 mr = 60092 m= 7651 mr = 22727 m= 1463 mr = 5838 m= 122 mr = 1051 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 792 time to turn everything in is 0.8500000 number of dielectric boundary points 69732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 16640 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) : 1.922592 object centre at (A) : 23.16350 3.435000 21.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2292126 0.4595330 midg,1,midg; midg,igrid,midg -0.1481674 0.2218544 1,midg,midg; igrid,midg,midg -0.1860629 -0.2209209 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 1.090000 now iterating at: 10:33:36 rms-change max change #iterations 9.063599 367.5352 at 10iterations 5.278390 116.5334 at 20iterations 3.059905 60.18954 at 30iterations 1.766020 36.20727 at 40iterations 1.019547 20.05314 at 50iterations 0.5883185 12.08918 at 60iterations 0.3385575 6.785033 at 70iterations 0.1942642 3.426377 at 80iterations 0.1117145 2.217510 at 90iterations 6.4213343E-02 1.239256 at 100iterations 3.6810532E-02 0.7036762 at 110iterations 2.1169949E-02 0.4203262 at 120iterations 1.2163137E-02 0.2191720 at 130iterations 6.9736703E-03 0.1346073 at 140iterations 4.0071504E-03 7.8676224E-02 at 150iterations 2.2955965E-03 4.5837402E-02 at 160iterations 1.3183708E-03 2.3937225E-02 at 170iterations 7.5665262E-04 1.5327454E-02 at 180iterations finished qdiffx linear iterations at : 10:33:47 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 7.5665262E-04 1.5327454E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 10:33:48 12.323u 0.200s 0:12.79 97.8% 0+0k 0+0io 0pf+0w