Wed Dec 21 14:21:00 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+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 Wed Dec 21 2011 at 14:21:00 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 = 1964 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: 0.6171020 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): -35.45700 10.13300 ymin,ymax (A): 1.710000 42.37400 zmin,zma (A): -27.72100 29.96800 x,y,z range (A): 45.59000 40.66400 57.68900 scale (grids/A): 0.6171020 object centre (A): -12.66200 22.04200 1.123501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.7721 centred at (gu) : 90.42401 89.20948 89.98341 assigned negative charge : -285.7723 centred at (gu) : 90.31925 89.38708 89.98234 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5225 nv = 96 ne = 84 npr = 39358 no. pairs analyzed = 39358 no. exposed pairs = 2471 no. arc points = 17131 no. surface atoms = 842 nbur = 1122 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 2959 m= 5 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1774 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6215 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3464435E-09 1.4326351E-09 midg,1,midg; midg,igrid,midg 1.1013483E-08 -5.6502683E-09 1,midg,midg; igrid,midg,midg -3.0651319E-09 6.6478338E-09 gauss-seidel spectral radius is 0.9863510 estimated iterations to convergence 70 setup time was (sec) 0.5600000 now iterating at: 14:21:01 rms-change max change #iterations 0.1058367 19.99827 at 10iterations 9.6227378E-03 1.581411 at 20iterations 8.6138392E-04 0.1420822 at 30iterations 7.9984937E-05 1.4460564E-02 at 40iterations 7.2832804E-06 1.0871887E-03 at 50iterations finished qdiffx linear iterations at : 14:21:04 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 7.2832804E-06 1.0871887E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 14:21:05 4.003u 0.247s 0:05.37 78.9% 0+0k 0+0io 6pf+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 Dec 21 2011 at 14:21:05 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 = 1964 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: 1.851306 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): -35.45700 10.13300 ymin,ymax (A): 1.710000 42.37400 zmin,zma (A): -27.72100 29.96800 x,y,z range (A): 45.59000 40.66400 57.68900 scale (grids/A): 1.851306 object centre (A): -12.66200 22.04200 1.123501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.7721 centred at (gu) : 91.27194 87.62849 89.95026 assigned negative charge : -285.7723 centred at (gu) : 90.95789 88.16143 89.94725 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 55834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17131 grid for indexing accessible points = 1.400000 m= 22386 mr = 38699 m= 3858 mr = 17541 m= 175 mr = 2560 m= 0 mr = 52 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 23401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14370 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) : 0.6171020 object centre at (A) : -12.66200 22.04200 1.123501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0083703E-02 2.0010091E-02 midg,1,midg; midg,igrid,midg 2.2788760E-03 -1.2741261E-02 1,midg,midg; igrid,midg,midg -6.9310861E-03 -2.3892452E-03 gauss-seidel spectral radius is 0.9984838 estimated iterations to convergence 204 setup time was (sec) 0.8300000 now iterating at: 14:21:06 rms-change max change #iterations 3.379839 177.7434 at 10iterations 1.518268 65.90695 at 20iterations 0.6829747 28.94227 at 30iterations 0.3074951 11.42173 at 40iterations 0.1376748 5.301022 at 50iterations 6.1561249E-02 2.315792 at 60iterations 2.7793845E-02 1.070152 at 70iterations 1.2535755E-02 0.4522476 at 80iterations 5.6239562E-03 0.1981468 at 90iterations 2.5301729E-03 9.7869873E-02 at 100iterations 1.1417869E-03 4.1458130E-02 at 110iterations 5.1240035E-04 1.7425537E-02 at 120iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 10.75000 # loops : 120 mean,max change (kT/e) : 5.1240035E-04 1.7425537E-02 energy calculations done at 10.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.95000 DelPhi exited at 14:21:19 10.952u 0.342s 0:13.81 81.7% 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 Wed Dec 21 2011 at 14:21:20 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 = 1964 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: 2.776959 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): -35.45700 10.13300 ymin,ymax (A): 1.710000 42.37400 zmin,zma (A): -27.72100 29.96800 x,y,z range (A): 45.59000 40.66400 57.68900 scale (grids/A): 2.776959 object centre (A): -12.66200 22.04200 1.123501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.7721 centred at (gu) : 91.90805 86.44281 89.92534 assigned negative charge : -285.7723 centred at (gu) : 91.43690 87.24221 89.92097 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 128683 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17131 grid for indexing accessible points = 1.400000 m= 69968 mr = 93311 m= 28558 mr = 58781 m= 7113 mr = 24288 m= 849 mr = 5571 m= 45 mr = 562 m= 0 mr = 29 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 52674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 14651 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) : 1.851306 object centre at (A) : -12.66200 22.04200 1.123501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6386475E-02 2.9003114E-02 midg,1,midg; midg,igrid,midg -2.9671989E-02 -0.1465375 1,midg,midg; igrid,midg,midg -9.7184904E-02 -7.3460057E-02 gauss-seidel spectral radius is 0.9991980 estimated iterations to convergence 279 setup time was (sec) 1.780000 now iterating at: 14:21:24 rms-change max change #iterations 8.077328 278.2288 at 10iterations 4.597955 140.3467 at 20iterations 2.593412 62.09241 at 30iterations 1.461535 31.15263 at 40iterations 0.8229094 18.19645 at 50iterations 0.4608052 11.09392 at 60iterations 0.2588898 5.573692 at 70iterations 0.1453608 3.002883 at 80iterations 8.1454955E-02 1.668454 at 90iterations 4.5745790E-02 0.9998131 at 100iterations 2.5686070E-02 0.5746918 at 110iterations 1.4410428E-02 0.3008478 at 120iterations 8.0458978E-03 0.1585679 at 130iterations 4.5270459E-03 0.1011658 at 140iterations 2.5301485E-03 4.9953461E-02 at 150iterations 1.4220226E-03 2.9434204E-02 at 160iterations 7.9711626E-04 1.5812874E-02 at 170iterations 4.4674912E-04 8.9902878E-03 at 180iterations finished qdiffx linear iterations at : 14:21:40 total time elapsed so far: 18.25000 # loops : 180 mean,max change (kT/e) : 4.4674912E-04 8.9902878E-03 energy calculations done at 18.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.45000 DelPhi exited at 14:21:43 18.456u 0.608s 0:23.43 81.3% 0+0k 0+0io 0pf+0w