Sun Oct 9 14:15:37 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 14:15:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2522 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: 0.6453719 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): -1.621000 45.95900 ymin,ymax (A): 10.27000 56.03500 zmin,zma (A): 10.50600 65.66800 x,y,z range (A): 47.58000 45.76500 55.16200 scale (grids/A): 0.6453719 object centre (A): 22.16900 33.15250 38.08700 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.500019 assigned positive charge : 380.6889 centred at (gu) : 88.39958 91.54182 89.97662 assigned negative charge : -371.1898 centred at (gu) : 88.30138 91.41908 89.86541 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7085 nv = 96 ne = 84 npr = 50869 no. pairs analyzed = 50869 no. exposed pairs = 3209 no. arc points = 22218 no. surface atoms = 1073 nbur = 1449 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 3790 m= 2 mr = 40 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 0.3600000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2258 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8403 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5765603E-09 2.9969183E-08 midg,1,midg; midg,igrid,midg 2.5221858E-10 4.3799254E-08 1,midg,midg; igrid,midg,midg 4.2185375E-09 2.0421961E-08 gauss-seidel spectral radius is 0.9875538 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 14:15:37 rms-change max change #iterations 0.1448840 24.94888 at 10iterations 1.4630055E-02 1.861775 at 20iterations 1.4606318E-03 0.2171516 at 30iterations 1.5207739E-04 2.3014069E-02 at 40iterations 1.7238681E-05 2.1715164E-03 at 50iterations finished qdiffx linear iterations at : 14:15:40 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.7238681E-05 2.1715164E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:15:40 3.407u 0.161s 0:03.85 92.4% 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 Sun Oct 9 2011 at 14:15:40 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 = 2522 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.936116 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): -1.621000 45.95900 ymin,ymax (A): 10.27000 56.03500 zmin,zma (A): 10.50600 65.66800 x,y,z range (A): 47.58000 45.76500 55.16200 scale (grids/A): 1.936116 object centre (A): 22.16900 33.15250 38.08700 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.500019 assigned positive charge : 380.6889 centred at (gu) : 85.19804 94.62481 89.92933 assigned negative charge : -371.1898 centred at (gu) : 84.90395 94.25725 89.59612 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 76295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22218 grid for indexing accessible points = 1.400000 m= 27415 mr = 52584 m= 4121 mr = 19472 m= 228 mr = 2323 m= 5 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 334 time to turn everything in is 0.5900000 number of dielectric boundary points 33627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18768 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) : 0.6453719 object centre at (A) : 22.16900 33.15250 38.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1646721E-02 3.4796447E-02 midg,1,midg; midg,igrid,midg -1.4640545E-02 1.5780732E-02 1,midg,midg; igrid,midg,midg 2.2209758E-02 3.7814405E-02 gauss-seidel spectral radius is 0.9986742 estimated iterations to convergence 218 setup time was (sec) 0.8800000 now iterating at: 14:15:42 rms-change max change #iterations 4.277382 173.0732 at 10iterations 2.024354 70.33507 at 20iterations 0.9566115 31.70314 at 30iterations 0.4514561 14.08804 at 40iterations 0.2141933 6.276605 at 50iterations 0.1012602 3.365451 at 60iterations 4.8093714E-02 1.341742 at 70iterations 2.2710072E-02 0.7804356 at 80iterations 1.0776036E-02 0.3059322 at 90iterations 5.0908579E-03 0.1546457 at 100iterations 2.4124742E-03 7.4619293E-02 at 110iterations 1.1439382E-03 3.4207344E-02 at 120iterations finished qdiffx linear iterations at : 14:15:48 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 1.1439382E-03 3.4207344E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 14:15:49 7.578u 0.175s 0:08.04 96.2% 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 14:15:49 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 = 2522 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.904173 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): -1.621000 45.95900 ymin,ymax (A): 10.27000 56.03500 zmin,zma (A): 10.50600 65.66800 x,y,z range (A): 47.58000 45.76500 55.16200 scale (grids/A): 2.904173 object centre (A): 22.16900 33.15250 38.08700 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.500019 assigned positive charge : 380.6889 centred at (gu) : 82.79701 96.93707 89.89395 assigned negative charge : -371.1898 centred at (gu) : 82.35588 96.38586 89.39405 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 176169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22218 grid for indexing accessible points = 1.400000 m= 88820 mr = 127401 m= 31498 mr = 71463 m= 7244 mr = 24418 m= 912 mr = 5014 m= 44 mr = 532 m= 0 mr = 10 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1070 time to turn everything in is 1.510000 number of dielectric boundary points 75849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19072 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) : 1.936116 object centre at (A) : 22.16900 33.15250 38.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9084186E-02 0.1609754 midg,1,midg; midg,igrid,midg -0.1267780 0.1258778 1,midg,midg; igrid,midg,midg 0.1977565 0.4062401 gauss-seidel spectral radius is 0.9992685 estimated iterations to convergence 292 setup time was (sec) 1.830000 now iterating at: 14:15:51 rms-change max change #iterations 10.03803 439.6421 at 10iterations 5.876355 132.2890 at 20iterations 3.432773 69.56944 at 30iterations 2.001673 43.63895 at 40iterations 1.163097 22.61520 at 50iterations 0.6747188 12.21990 at 60iterations 0.3905277 7.343687 at 70iterations 0.2266424 4.151594 at 80iterations 0.1309655 2.259453 at 90iterations 7.5746156E-02 1.353992 at 100iterations 4.3637216E-02 0.8251591 at 110iterations 2.5239449E-02 0.4667807 at 120iterations 1.4549901E-02 0.2613792 at 130iterations 8.4204739E-03 0.1710835 at 140iterations 4.8515927E-03 8.4566116E-02 at 150iterations 2.7973931E-03 5.3649902E-02 at 160iterations 1.6167104E-03 2.7385950E-02 at 170iterations 9.3314290E-04 1.6769409E-02 at 180iterations finished qdiffx linear iterations at : 14:16:01 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 9.3314290E-04 1.6769409E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 14:16:01 12.290u 0.182s 0:12.75 97.8% 0+0k 0+0io 0pf+0w