Sun Oct 9 17:31:59 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 17:31:59 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5719059 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): -11.08600 51.16200 ymin,ymax (A): -11.97100 40.54200 zmin,zma (A): 20.19100 75.86200 x,y,z range (A): 62.24800 52.51300 55.67100 scale (grids/A): 0.5719059 object centre (A): 20.03800 14.28550 48.02650 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621018 assigned positive charge : 494.8149 centred at (gu) : 90.93879 89.87860 87.87888 assigned negative charge : -491.1951 centred at (gu) : 90.84039 90.00162 87.83380 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7011 nv = 96 ne = 84 npr = 62805 no. pairs analyzed = 62805 no. exposed pairs = 4296 no. arc points = 30555 no. surface atoms = 1433 nbur = 1775 mkacc time = 0.1400000 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 = 1.484000 m= 316 mr = 3510 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2918 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3449411E-10 8.6344154E-10 midg,1,midg; midg,igrid,midg 2.9063758E-09 -1.6579081E-09 1,midg,midg; igrid,midg,midg -9.8644681E-10 2.9833636E-09 gauss-seidel spectral radius is 0.9842449 estimated iterations to convergence 65 setup time was (sec) 0.5700000 now iterating at: 17:32:00 rms-change max change #iterations 9.6438400E-02 14.74358 at 10iterations 7.3259398E-03 1.078959 at 20iterations 5.4396084E-04 0.1008873 at 30iterations 4.9130329E-05 7.2810650E-03 at 40iterations 1.2046607E-05 1.6822815E-03 at 50iterations finished qdiffx linear iterations at : 17:32:03 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.2046607E-05 1.6822815E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 17:32:03 3.497u 0.232s 0:04.03 92.3% 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 17:32:03 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.715718 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): -11.08600 51.16200 ymin,ymax (A): -11.97100 40.54200 zmin,zma (A): 20.19100 75.86200 x,y,z range (A): 62.24800 52.51300 55.67100 scale (grids/A): 1.715718 object centre (A): 20.03800 14.28550 48.02650 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621018 assigned positive charge : 494.8149 centred at (gu) : 92.81533 89.63533 83.63597 assigned negative charge : -491.1951 centred at (gu) : 92.52071 90.00443 83.50097 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30555 grid for indexing accessible points = 1.400000 m= 25511 mr = 50835 m= 3196 mr = 17187 m= 125 mr = 1585 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 35461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 279 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 23692 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) : 0.5719059 object centre at (A) : 20.03800 14.28550 48.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4412554E-03 5.7245190E-03 midg,1,midg; midg,igrid,midg 1.9505503E-02 -1.0347632E-02 1,midg,midg; igrid,midg,midg -7.6316642E-03 1.8599233E-02 gauss-seidel spectral radius is 0.9983872 estimated iterations to convergence 198 setup time was (sec) 0.8500000 now iterating at: 17:32:04 rms-change max change #iterations 3.944330 187.5188 at 10iterations 1.731989 63.25529 at 20iterations 0.7638960 31.09731 at 30iterations 0.3357001 11.96843 at 40iterations 0.1479126 4.963182 at 50iterations 6.4800799E-02 2.269346 at 60iterations 2.8675191E-02 0.9499533 at 70iterations 1.2564697E-02 0.4187946 at 80iterations 5.5334866E-03 0.1958990 at 90iterations 2.4574869E-03 8.6498260E-02 at 100iterations 1.1125784E-03 3.7742615E-02 at 110iterations 5.3606404E-04 2.0879745E-02 at 120iterations finished qdiffx linear iterations at : 17:32:11 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 5.3606404E-04 2.0879745E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 17:32:12 7.747u 0.246s 0:08.31 96.0% 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 17:32:12 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3208 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.573577 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): -11.08600 51.16200 ymin,ymax (A): -11.97100 40.54200 zmin,zma (A): 20.19100 75.86200 x,y,z range (A): 62.24800 52.51300 55.67100 scale (grids/A): 2.573577 object centre (A): 20.03800 14.28550 48.02650 number of atom coordinates read : 3208 total number of charged atoms : 3061 net assigned charge : 3.621018 assigned positive charge : 494.8149 centred at (gu) : 94.22291 89.45291 80.45377 assigned negative charge : -491.1951 centred at (gu) : 93.78098 90.00661 80.25134 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 176604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30555 grid for indexing accessible points = 1.400000 m= 84752 mr = 124550 m= 27291 mr = 66079 m= 5206 mr = 20088 m= 465 mr = 3357 m= 11 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 80037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 24473 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) : 1.715718 object centre at (A) : 20.03800 14.28550 48.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1302219 6.7470223E-02 midg,1,midg; midg,igrid,midg 0.2661117 -0.2085324 1,midg,midg; igrid,midg,midg 9.8984361E-02 0.2249147 gauss-seidel spectral radius is 0.9992126 estimated iterations to convergence 281 setup time was (sec) 1.660000 now iterating at: 17:32:13 rms-change max change #iterations 10.14714 320.3690 at 10iterations 5.967943 155.2147 at 20iterations 3.458330 85.09132 at 30iterations 1.995621 48.69300 at 40iterations 1.145742 23.59930 at 50iterations 0.6559008 13.34740 at 60iterations 0.3745600 7.945377 at 70iterations 0.2136126 4.805542 at 80iterations 0.1211528 2.514745 at 90iterations 6.8934873E-02 1.573696 at 100iterations 3.9157148E-02 0.8218231 at 110iterations 2.2223864E-02 0.4594641 at 120iterations 1.2655502E-02 0.2811127 at 130iterations 7.1992013E-03 0.1410646 at 140iterations 4.1535916E-03 8.3160400E-02 at 150iterations 2.4471560E-03 4.7276020E-02 at 160iterations 1.5051047E-03 3.5933971E-02 at 170iterations 9.9824346E-04 2.0981789E-02 at 180iterations finished qdiffx linear iterations at : 17:32:25 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 9.9824346E-04 2.0981789E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 17:32:25 12.988u 0.272s 0:13.55 97.7% 0+0k 0+0io 0pf+0w