Tue Nov 22 14:11:45 PST 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 Tue Nov 22 2011 at 14:11:50 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASL 30 has a net charge of -0.1000 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: 0.6022466 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): -9.191999 49.92000 ymin,ymax (A): -18.68400 21.76500 zmin,zma (A): -7.692000 34.50700 x,y,z range (A): 59.11200 40.44900 42.19900 scale (grids/A): 0.6022466 object centre (A): 20.36400 1.540500 13.40750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.900015 assigned positive charge : 293.3019 centred at (gu) : 89.93007 89.80658 89.53378 assigned negative charge : -288.4023 centred at (gu) : 89.90196 89.89283 89.41182 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4854 nv = 96 ne = 84 npr = 39734 no. pairs analyzed = 39734 no. exposed pairs = 2469 no. arc points = 17383 no. surface atoms = 849 nbur = 1117 mkacc time = 7.0000000E-02 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= 231 mr = 2644 m= 0 mr = 17 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5879 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4849809E-09 5.1974083E-09 midg,1,midg; midg,igrid,midg 4.9708340E-09 -2.4064201E-10 1,midg,midg; igrid,midg,midg 1.4779776E-09 3.0430141E-09 gauss-seidel spectral radius is 0.9856778 estimated iterations to convergence 69 setup time was (sec) 0.3600000 now iterating at: 14:11:53 rms-change max change #iterations 9.9530764E-02 17.71755 at 10iterations 8.6244568E-03 1.606232 at 20iterations 7.2361733E-04 0.1229973 at 30iterations 6.0375620E-05 1.1690140E-02 at 40iterations 5.2416817E-06 9.9563599E-04 at 50iterations finished qdiffx linear iterations at : 14:12:03 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 5.2416817E-06 9.9563599E-04 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 14:12:05 3.591u 0.205s 0:15.50 24.4% 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 Tue Nov 22 2011 at 14:12:07 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASL 30 has a net charge of -0.1000 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: 1.806740 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): -9.191999 49.92000 ymin,ymax (A): -18.68400 21.76500 zmin,zma (A): -7.692000 34.50700 x,y,z range (A): 59.11200 40.44900 42.19900 scale (grids/A): 1.806740 object centre (A): 20.36400 1.540500 13.40750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.900015 assigned positive charge : 293.3019 centred at (gu) : 89.79001 89.41992 88.60122 assigned negative charge : -288.4023 centred at (gu) : 89.70618 89.67864 88.23549 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17383 grid for indexing accessible points = 1.400000 m= 17779 mr = 35728 m= 2196 mr = 13147 m= 80 mr = 1269 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 595 time to turn everything in is 0.2700000 number of dielectric boundary points 22339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14298 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) : 0.6022466 object centre at (A) : 20.36400 1.540500 13.40750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0232173E-03 1.0685522E-02 midg,1,midg; midg,igrid,midg 7.7094524E-03 1.9655798E-03 1,midg,midg; igrid,midg,midg 2.7192308E-02 3.3396766E-02 gauss-seidel spectral radius is 0.9984111 estimated iterations to convergence 199 setup time was (sec) 0.5000000 now iterating at: 14:12:11 rms-change max change #iterations 3.314908 199.5554 at 10iterations 1.462358 58.25251 at 20iterations 0.6449830 25.25877 at 30iterations 0.2836209 10.86532 at 40iterations 0.1250519 4.719475 at 50iterations 5.5269741E-02 2.286129 at 60iterations 2.4352074E-02 0.9399261 at 70iterations 1.0745950E-02 0.4259238 at 80iterations 4.7381930E-03 0.1900940 at 90iterations 2.0856729E-03 7.9339981E-02 at 100iterations 9.2034705E-04 3.3401489E-02 at 110iterations 4.0578868E-04 1.4465332E-02 at 120iterations finished qdiffx linear iterations at : 14:12:34 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 4.0578868E-04 1.4465332E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 14:12:35 8.197u 0.222s 0:28.50 29.5% 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 Tue Nov 22 2011 at 14:12:37 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASL 30 has a net charge of -0.1000 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: 2.710110 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): -9.191999 49.92000 ymin,ymax (A): -18.68400 21.76500 zmin,zma (A): -7.692000 34.50700 x,y,z range (A): 59.11200 40.44900 42.19900 scale (grids/A): 2.710110 object centre (A): 20.36400 1.540500 13.40750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 4.900015 assigned positive charge : 293.3019 centred at (gu) : 89.68502 89.12975 87.90177 assigned negative charge : -288.4023 centred at (gu) : 89.55930 89.51804 87.35323 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 121449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17383 grid for indexing accessible points = 1.400000 m= 59166 mr = 86819 m= 19416 mr = 48469 m= 3697 mr = 15553 m= 358 mr = 2664 m= 18 mr = 214 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1979 time to turn everything in is 0.7200000 number of dielectric boundary points 50386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 14669 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) : 1.806740 object centre at (A) : 20.36400 1.540500 13.40750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4966682E-03 9.0687364E-02 midg,1,midg; midg,igrid,midg 5.8793392E-02 5.5099059E-02 1,midg,midg; igrid,midg,midg 0.3238820 0.3914668 gauss-seidel spectral radius is 0.9991776 estimated iterations to convergence 275 setup time was (sec) 1.040000 now iterating at: 14:12:43 rms-change max change #iterations 7.986695 305.0154 at 10iterations 4.526262 120.8735 at 20iterations 2.537838 58.78859 at 30iterations 1.415292 32.41347 at 40iterations 0.7899233 18.42191 at 50iterations 0.4408287 9.967078 at 60iterations 0.2459502 6.009647 at 70iterations 0.1368099 3.172907 at 80iterations 7.6166689E-02 1.626274 at 90iterations 4.2397309E-02 0.9954424 at 100iterations 2.3574201E-02 0.5489702 at 110iterations 1.3143302E-02 0.2917290 at 120iterations 7.2872904E-03 0.1691551 at 130iterations 4.0504704E-03 8.5079193E-02 at 140iterations 2.2566826E-03 4.8309326E-02 at 150iterations 1.2513974E-03 2.8498650E-02 at 160iterations 6.9821655E-04 1.4989853E-02 at 170iterations 3.8901481E-04 8.2359314E-03 at 180iterations finished qdiffx linear iterations at : 14:13:23 total time elapsed so far: 14.04000 # loops : 180 mean,max change (kT/e) : 3.8901481E-04 8.2359314E-03 energy calculations done at 14.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.17000 DelPhi exited at 14:13:24 14.173u 0.314s 0:47.45 30.5% 0+0k 0+0io 0pf+0w