Sat Oct 15 15:13:26 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 Sat Oct 15 2011 at 15:13:26 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6085470 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): -7.791000 50.70900 ymin,ymax (A): 7.296999 61.76500 zmin,zma (A): 1.057000 55.92100 x,y,z range (A): 58.50000 54.46800 54.86400 scale (grids/A): 0.6085470 object centre (A): 21.45900 34.53100 28.48900 number of atom coordinates read : 2809 total number of charged atoms : 2601 net assigned charge : 6.500016 assigned positive charge : 415.2617 centred at (gu) : 90.23932 90.91612 90.94611 assigned negative charge : -408.7624 centred at (gu) : 90.52222 90.78423 90.78197 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6675 nv = 96 ne = 84 npr = 57989 no. pairs analyzed = 57989 no. exposed pairs = 3415 no. arc points = 23883 no. surface atoms = 1170 nbur = 1639 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3541 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2281 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8172 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8060932E-09 1.4371623E-08 midg,1,midg; midg,igrid,midg -2.4831479E-09 1.2356622E-08 1,midg,midg; igrid,midg,midg 1.6328274E-08 -1.1622201E-08 gauss-seidel spectral radius is 0.9860343 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 15:13:27 rms-change max change #iterations 0.1212693 17.91763 at 10iterations 1.0814537E-02 1.662547 at 20iterations 1.0990084E-03 0.1516905 at 30iterations 2.2096398E-04 2.6985168E-02 at 40iterations 7.6956072E-05 8.7795258E-03 at 50iterations finished qdiffx linear iterations at : 15:13:33 total time elapsed so far: 5.540000 # loops : 50 mean,max change (kT/e) : 7.6956072E-05 8.7795258E-03 energy calculations done at 5.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.720000 DelPhi exited at 15:13:36 5.728u 0.412s 0:09.86 62.1% 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 Sat Oct 15 2011 at 15:13:36 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.825641 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): -7.791000 50.70900 ymin,ymax (A): 7.296999 61.76500 zmin,zma (A): 1.057000 55.92100 x,y,z range (A): 58.50000 54.46800 54.86400 scale (grids/A): 1.825641 object centre (A): 21.45900 34.53100 28.48900 number of atom coordinates read : 2809 total number of charged atoms : 2601 net assigned charge : 6.500016 assigned positive charge : 415.2617 centred at (gu) : 90.71735 92.74773 92.83777 assigned negative charge : -408.7624 centred at (gu) : 91.56612 92.35228 92.34562 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23883 grid for indexing accessible points = 1.400000 m= 26746 mr = 48752 m= 4726 mr = 19563 m= 237 mr = 2986 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 31698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20385 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) : 0.6085470 object centre at (A) : 21.45900 34.53100 28.48900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1076846E-02 7.0898317E-02 midg,1,midg; midg,igrid,midg -1.8817149E-02 9.4955758E-04 1,midg,midg; igrid,midg,midg 6.0276859E-02 -5.5145457E-02 gauss-seidel spectral radius is 0.9985397 estimated iterations to convergence 207 setup time was (sec) 1.010000 now iterating at: 15:13:37 rms-change max change #iterations 4.030817 181.2353 at 10iterations 1.834192 77.98992 at 20iterations 0.8366613 30.14634 at 30iterations 0.3824252 12.49742 at 40iterations 0.1746092 5.751536 at 50iterations 7.9805382E-02 2.634552 at 60iterations 3.6579762E-02 1.326175 at 70iterations 1.6665034E-02 0.5227413 at 80iterations 7.6437555E-03 0.2469425 at 90iterations 3.5286739E-03 0.1152821 at 100iterations 1.6411940E-03 5.3391457E-02 at 110iterations 7.8757951E-04 2.4857283E-02 at 120iterations finished qdiffx linear iterations at : 15:13:55 total time elapsed so far: 13.95000 # loops : 120 mean,max change (kT/e) : 7.8757951E-04 2.4857283E-02 energy calculations done at 13.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.13000 DelPhi exited at 15:13:55 14.131u 0.523s 0:19.61 74.7% 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 Sat Oct 15 2011 at 15:13:55 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.738461 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): -7.791000 50.70900 ymin,ymax (A): 7.296999 61.76500 zmin,zma (A): 1.057000 55.92100 x,y,z range (A): 58.50000 54.46800 54.86400 scale (grids/A): 2.738461 object centre (A): 21.45900 34.53100 28.48900 number of atom coordinates read : 2809 total number of charged atoms : 2601 net assigned charge : 6.500016 assigned positive charge : 415.2617 centred at (gu) : 91.07575 94.12139 94.25648 assigned negative charge : -408.7624 centred at (gu) : 92.34918 93.52831 93.51838 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 164383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23883 grid for indexing accessible points = 1.400000 m= 84642 mr = 118076 m= 33143 mr = 68718 m= 8440 mr = 26578 m= 1106 mr = 6310 m= 52 mr = 668 m= 0 mr = 5 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 71411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 20798 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) : 1.825641 object centre at (A) : 21.45900 34.53100 28.48900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1542415 0.9978380 midg,1,midg; midg,igrid,midg -0.2786902 -0.1219191 1,midg,midg; igrid,midg,midg 1.098320 -0.8105134 gauss-seidel spectral radius is 0.9992356 estimated iterations to convergence 286 setup time was (sec) 2.070000 now iterating at: 15:13:58 rms-change max change #iterations 9.705787 376.8647 at 10iterations 5.680194 143.5374 at 20iterations 3.293810 100.3400 at 30iterations 1.905006 42.97882 at 40iterations 1.100354 22.16159 at 50iterations 0.6313810 11.67346 at 60iterations 0.3625695 7.329453 at 70iterations 0.2077887 4.027746 at 80iterations 0.1189063 2.331896 at 90iterations 6.7958884E-02 1.392340 at 100iterations 3.8892217E-02 0.7822113 at 110iterations 2.2215953E-02 0.4563885 at 120iterations 1.2659184E-02 0.2335529 at 130iterations 7.2418354E-03 0.1370206 at 140iterations 4.1320967E-03 8.3667755E-02 at 150iterations 2.3554249E-03 4.8776627E-02 at 160iterations 1.3451620E-03 2.5497437E-02 at 170iterations 7.7045360E-04 1.5108109E-02 at 180iterations finished qdiffx linear iterations at : 15:14:23 total time elapsed so far: 23.50000 # loops : 180 mean,max change (kT/e) : 7.7045360E-04 1.5108109E-02 energy calculations done at 23.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.65000 DelPhi exited at 15:14:24 23.657u 0.594s 0:28.16 86.0% 0+0k 0+0io 0pf+0w