Sun Oct 9 12:28:47 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 12:28:47 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 = 2358 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: 0.7095166 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): -5.532000 44.15200 ymin,ymax (A): -13.88100 36.29400 zmin,zma (A): 2.087000 44.94600 x,y,z range (A): 49.68400 50.17500 42.85900 scale (grids/A): 0.7095166 object centre (A): 19.31000 11.20650 23.51650 number of atom coordinates read : 2358 total number of charged atoms : 2217 net assigned charge : 3.500013 assigned positive charge : 359.2311 centred at (gu) : 89.24262 91.11600 90.64611 assigned negative charge : -355.7316 centred at (gu) : 89.27144 91.29623 90.67836 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7989 nv = 96 ne = 84 npr = 47855 no. pairs analyzed = 47855 no. exposed pairs = 2905 no. arc points = 20097 no. surface atoms = 972 nbur = 1386 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 511 mr = 4522 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 0.2800000 number of dielectric boundary points 3905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1902 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8970 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5351022E-08 1.4893072E-08 midg,1,midg; midg,igrid,midg 1.0992839E-07 -9.5256986E-08 1,midg,midg; igrid,midg,midg 5.7055228E-08 1.3458489E-08 gauss-seidel spectral radius is 0.9896723 estimated iterations to convergence 80 setup time was (sec) 0.5000000 now iterating at: 12:28:47 rms-change max change #iterations 0.2170005 28.53144 at 10iterations 2.7075930E-02 3.835861 at 20iterations 3.4589984E-03 0.4767580 at 30iterations 5.0034199E-04 7.5513840E-02 at 40iterations 9.7424585E-05 1.5829086E-02 at 50iterations finished qdiffx linear iterations at : 12:28:50 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 9.7424585E-05 1.5829086E-02 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 12:28:50 3.059u 0.126s 0:03.49 90.8% 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 12:28:50 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 2.128550 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): -5.532000 44.15200 ymin,ymax (A): -13.88100 36.29400 zmin,zma (A): 2.087000 44.94600 x,y,z range (A): 49.68400 50.17500 42.85900 scale (grids/A): 2.128550 object centre (A): 19.31000 11.20650 23.51650 number of atom coordinates read : 2358 total number of charged atoms : 2217 net assigned charge : 3.500013 assigned positive charge : 359.2311 centred at (gu) : 87.72723 93.34743 91.93790 assigned negative charge : -355.7316 centred at (gu) : 87.81415 93.88842 92.03484 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20097 grid for indexing accessible points = 1.400000 m= 32398 mr = 59071 m= 5928 mr = 24233 m= 599 mr = 3877 m= 14 mr = 346 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2909 time to turn everything in is 0.5800000 number of dielectric boundary points 35793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17606 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) : 0.7095166 object centre at (A) : 19.31000 11.20650 23.51650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3519916E-02 1.0326796E-02 midg,1,midg; midg,igrid,midg 2.5258824E-02 -6.1369926E-02 1,midg,midg; igrid,midg,midg 6.6906333E-02 -1.1767562E-02 gauss-seidel spectral radius is 0.9988672 estimated iterations to convergence 235 setup time was (sec) 0.8300000 now iterating at: 12:28:51 rms-change max change #iterations 5.009584 221.1821 at 10iterations 2.494673 87.68773 at 20iterations 1.246522 39.16799 at 30iterations 0.6249987 18.79119 at 40iterations 0.3138087 9.473816 at 50iterations 0.1568973 4.269463 at 60iterations 7.8661472E-02 2.196127 at 70iterations 3.9439335E-02 1.073318 at 80iterations 1.9870708E-02 0.6652589 at 90iterations 9.9917157E-03 0.2843256 at 100iterations 5.0194729E-03 0.1507454 at 110iterations 2.5464981E-03 6.9950104E-02 at 120iterations finished qdiffx linear iterations at : 12:28:57 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 2.5464981E-03 6.9950104E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 12:28:58 6.891u 0.161s 0:07.32 96.3% 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 12:28:58 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 = 2358 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: 3.192825 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): -5.532000 44.15200 ymin,ymax (A): -13.88100 36.29400 zmin,zma (A): 2.087000 44.94600 x,y,z range (A): 49.68400 50.17500 42.85900 scale (grids/A): 3.192825 object centre (A): 19.31000 11.20650 23.51650 number of atom coordinates read : 2358 total number of charged atoms : 2217 net assigned charge : 3.500013 assigned positive charge : 359.2311 centred at (gu) : 86.59097 95.02116 92.90673 assigned negative charge : -355.7316 centred at (gu) : 86.72112 95.83259 93.05212 start vw surface at 0.1400000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 194732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20097 grid for indexing accessible points = 1.400000 m= 102513 mr = 142847 m= 39821 mr = 84485 m= 11096 mr = 32318 m= 2320 mr = 8613 m= 346 mr = 1744 m= 12 mr = 248 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 10155 time to turn everything in is 1.840000 number of dielectric boundary points 80585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 17735 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) : 2.128550 object centre at (A) : 19.31000 11.20650 23.51650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4995702 -1.6234498E-02 midg,1,midg; midg,igrid,midg 0.5542133 -0.6192566 1,midg,midg; igrid,midg,midg 0.7194039 -0.4126201 gauss-seidel spectral radius is 0.9993058 estimated iterations to convergence 299 setup time was (sec) 2.130000 now iterating at: 12:29:00 rms-change max change #iterations 11.07199 485.6808 at 10iterations 6.569134 127.7360 at 20iterations 3.891503 74.61121 at 30iterations 2.292823 39.42604 at 40iterations 1.353635 22.14539 at 50iterations 0.7993665 13.48291 at 60iterations 0.4702531 8.241055 at 70iterations 0.2763339 4.589731 at 80iterations 0.1625330 2.890945 at 90iterations 9.5578343E-02 1.640298 at 100iterations 5.6092814E-02 0.9550171 at 110iterations 3.3061285E-02 0.5356216 at 120iterations 1.9530741E-02 0.3420868 at 130iterations 1.1588390E-02 0.2016525 at 140iterations 6.9666719E-03 0.1204796 at 150iterations 4.2596725E-03 7.6477051E-02 at 160iterations 2.6848405E-03 5.3726196E-02 at 170iterations 1.7712244E-03 3.3695221E-02 at 180iterations finished qdiffx linear iterations at : 12:29:09 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 1.7712244E-03 3.3695221E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 12:29:10 11.721u 0.169s 0:12.26 96.9% 0+0k 0+0io 0pf+0w