Wed Feb 15 08:54:33 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:34 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5940464 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): 82.28600 142.2140 ymin,ymax (A): 40.67000 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 54.68499 54.16400 scale (grids/A): 0.5940464 object centre (A): 112.2500 68.01250 0.6699991 number of atom coordinates read : 2782 total number of charged atoms : 2636 net assigned charge : -2.999983 assigned positive charge : 419.8685 centred at (gu) : 89.28838 90.60126 90.70058 assigned negative charge : -422.8693 centred at (gu) : 89.29302 90.54391 90.59225 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6457 nv = 96 ne = 84 npr = 56239 no. pairs analyzed = 56239 no. exposed pairs = 3634 no. arc points = 25680 no. surface atoms = 1223 nbur = 1559 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 302 mr = 3343 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2681 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0124855E-09 2.8768616E-09 midg,1,midg; midg,igrid,midg -2.6146882E-09 9.1098912E-10 1,midg,midg; igrid,midg,midg -1.1026293E-09 -1.0657518E-09 gauss-seidel spectral radius is 0.9853523 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 08:54:34 rms-change max change #iterations 0.1045495 16.58086 at 10iterations 9.0008564E-03 1.567466 at 20iterations 1.1457955E-03 0.1715450 at 30iterations 3.0200352E-04 5.3836823E-02 at 40iterations 9.9514706E-05 1.8013000E-02 at 50iterations finished qdiffx linear iterations at : 08:54:38 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 9.9514706E-05 1.8013000E-02 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 08:54:38 3.689u 0.272s 0:04.63 85.3% 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 Wed Feb 15 2012 at 08:54:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.782139 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): 82.28600 142.2140 ymin,ymax (A): 40.67000 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 54.68499 54.16400 scale (grids/A): 1.782139 object centre (A): 112.2500 68.01250 0.6699991 number of atom coordinates read : 2782 total number of charged atoms : 2636 net assigned charge : -2.999983 assigned positive charge : 419.8685 centred at (gu) : 87.86417 91.80310 92.10113 assigned negative charge : -422.8693 centred at (gu) : 87.87878 91.63144 91.77666 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25680 grid for indexing accessible points = 1.400000 m= 23383 mr = 48473 m= 3033 mr = 16084 m= 173 mr = 1563 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 31665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20529 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) : 0.5940464 object centre at (A) : 112.2500 68.01250 0.6699991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0366182E-02 9.0154083E-03 midg,1,midg; midg,igrid,midg -1.1849371E-02 3.0195056E-03 1,midg,midg; igrid,midg,midg -4.3699007E-02 -6.1722081E-03 gauss-seidel spectral radius is 0.9984637 estimated iterations to convergence 202 setup time was (sec) 0.7000000 now iterating at: 08:54:40 rms-change max change #iterations 3.935809 199.9099 at 10iterations 1.756978 82.42767 at 20iterations 0.7842880 30.11099 at 30iterations 0.3513879 11.24463 at 40iterations 0.1574885 5.954269 at 50iterations 7.0490912E-02 2.305984 at 60iterations 3.1675320E-02 1.144232 at 70iterations 1.4284929E-02 0.4731774 at 80iterations 6.4802617E-03 0.2271948 at 90iterations 2.9995760E-03 0.1039017 at 100iterations 1.4342649E-03 5.2185059E-02 at 110iterations 7.3549262E-04 2.7500153E-02 at 120iterations finished qdiffx linear iterations at : 08:54:49 total time elapsed so far: 9.870000 # loops : 120 mean,max change (kT/e) : 7.3549262E-04 2.7500153E-02 energy calculations done at 9.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 08:54:50 10.005u 0.389s 0:11.11 93.4% 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 Wed Feb 15 2012 at 08:54:50 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 has a net charge of -2.0000 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: 2.673208 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): 82.28600 142.2140 ymin,ymax (A): 40.67000 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 54.68499 54.16400 scale (grids/A): 2.673208 object centre (A): 112.2500 68.01250 0.6699991 number of atom coordinates read : 2782 total number of charged atoms : 2636 net assigned charge : -2.999983 assigned positive charge : 419.8685 centred at (gu) : 86.79614 92.70454 93.15155 assigned negative charge : -422.8693 centred at (gu) : 86.81813 92.44713 92.66494 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 165023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25680 grid for indexing accessible points = 1.400000 m= 78918 mr = 118361 m= 24727 mr = 62575 m= 5229 mr = 18391 m= 643 mr = 3416 m= 22 mr = 361 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 71458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 21077 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) : 1.782139 object centre at (A) : 112.2500 68.01250 0.6699991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4586357 0.1040493 midg,1,midg; midg,igrid,midg -0.1698849 8.5470416E-02 1,midg,midg; igrid,midg,midg -1.094187 -2.2185635E-02 gauss-seidel spectral radius is 0.9992232 estimated iterations to convergence 283 setup time was (sec) 1.150000 now iterating at: 08:54:55 rms-change max change #iterations 9.662261 444.5163 at 10iterations 5.666889 171.8864 at 20iterations 3.283340 81.16923 at 30iterations 1.889976 44.91069 at 40iterations 1.085466 25.62685 at 50iterations 0.6230474 14.48111 at 60iterations 0.3552179 8.681495 at 70iterations 0.2032237 3.939969 at 80iterations 0.1155328 2.265345 at 90iterations 6.5880358E-02 1.335709 at 100iterations 3.7446190E-02 0.7885380 at 110iterations 2.1335199E-02 0.4200172 at 120iterations 1.2137139E-02 0.2314467 at 130iterations 6.9125919E-03 0.1319988 at 140iterations 3.9442121E-03 7.7203751E-02 at 150iterations 2.2703861E-03 4.2972565E-02 at 160iterations 1.3207083E-03 2.8282166E-02 at 170iterations 7.8388181E-04 1.6450882E-02 at 180iterations finished qdiffx linear iterations at : 08:55:07 total time elapsed so far: 12.54000 # loops : 180 mean,max change (kT/e) : 7.8388181E-04 1.6450882E-02 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 08:55:07 12.684u 0.211s 0:17.62 73.1% 0+0k 0+0io 0pf+0w