Tue Oct 11 03:14:01 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 Tue Oct 11 2011 at 03:14:02 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 = 2172 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: 0.7119288 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): 19.30400 66.56800 ymin,ymax (A): 16.42000 61.19400 zmin,zma (A): 4.610000 54.61500 x,y,z range (A): 47.26400 44.77400 50.00500 scale (grids/A): 0.7119288 object centre (A): 42.93600 38.80700 29.61250 number of atom coordinates read : 2172 total number of charged atoms : 2046 net assigned charge : 2.000009 assigned positive charge : 321.7015 centred at (gu) : 90.69239 90.66803 90.39206 assigned negative charge : -319.7019 centred at (gu) : 90.63617 90.71586 90.59790 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7491 nv = 96 ne = 84 npr = 45398 no. pairs analyzed = 45398 no. exposed pairs = 2776 no. arc points = 19357 no. surface atoms = 927 nbur = 1245 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 518 mr = 4126 m= 6 mr = 92 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 0.2600000 number of dielectric boundary points 3797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1661 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8297 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2235195E-07 -1.0623588E-07 midg,1,midg; midg,igrid,midg 4.0406796E-08 -8.7744523E-09 1,midg,midg; igrid,midg,midg -1.0564997E-08 5.7930873E-08 gauss-seidel spectral radius is 0.9897299 estimated iterations to convergence 80 setup time was (sec) 0.6100000 now iterating at: 03:14:03 rms-change max change #iterations 0.2132900 29.08859 at 10iterations 2.6069049E-02 3.783646 at 20iterations 3.3275764E-03 0.4013596 at 30iterations 4.4828522E-04 6.2891960E-02 at 40iterations 6.9654408E-05 9.5734596E-03 at 50iterations finished qdiffx linear iterations at : 03:14:07 total time elapsed so far: 4.850000 # loops : 50 mean,max change (kT/e) : 6.9654408E-05 9.5734596E-03 energy calculations done at 4.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.020000 DelPhi exited at 03:14:07 5.029u 0.460s 0:05.90 92.8% 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 Tue Oct 11 2011 at 03:14:07 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 = 2172 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: 2.135787 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): 19.30400 66.56800 ymin,ymax (A): 16.42000 61.19400 zmin,zma (A): 4.610000 54.61500 x,y,z range (A): 47.26400 44.77400 50.00500 scale (grids/A): 2.135787 object centre (A): 42.93600 38.80700 29.61250 number of atom coordinates read : 2172 total number of charged atoms : 2046 net assigned charge : 2.000009 assigned positive charge : 321.7015 centred at (gu) : 92.07706 92.00393 91.17622 assigned negative charge : -319.7019 centred at (gu) : 91.90833 92.14771 91.79356 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19357 grid for indexing accessible points = 1.400000 m= 30826 mr = 55207 m= 6335 mr = 22886 m= 656 mr = 4128 m= 28 mr = 298 m= 0 mr = 1 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 16236 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) : 0.7119288 object centre at (A) : 42.93600 38.80700 29.61250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3290981E-02 -7.4396856E-02 midg,1,midg; midg,igrid,midg 1.8535612E-02 -1.2581556E-02 1,midg,midg; igrid,midg,midg -3.3876795E-02 -4.3853667E-02 gauss-seidel spectral radius is 0.9988620 estimated iterations to convergence 235 setup time was (sec) 1.020000 now iterating at: 03:14:09 rms-change max change #iterations 4.772861 207.8413 at 10iterations 2.385570 79.83938 at 20iterations 1.198794 39.40309 at 30iterations 0.6008921 18.30251 at 40iterations 0.3012877 8.770422 at 50iterations 0.1509833 4.509082 at 60iterations 7.5647995E-02 2.155300 at 70iterations 3.7903726E-02 1.124031 at 80iterations 1.8969100E-02 0.5569077 at 90iterations 9.5272027E-03 0.2919388 at 100iterations 4.7824397E-03 0.1344604 at 110iterations 2.4081012E-03 6.8921089E-02 at 120iterations finished qdiffx linear iterations at : 03:14:20 total time elapsed so far: 12.01000 # loops : 120 mean,max change (kT/e) : 2.4081012E-03 6.8921089E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 03:14:21 12.199u 0.487s 0:13.08 96.8% 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 Tue Oct 11 2011 at 03:14:21 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 = 2172 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: 3.203680 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): 19.30400 66.56800 ymin,ymax (A): 16.42000 61.19400 zmin,zma (A): 4.610000 54.61500 x,y,z range (A): 47.26400 44.77400 50.00500 scale (grids/A): 3.203680 object centre (A): 42.93600 38.80700 29.61250 number of atom coordinates read : 2172 total number of charged atoms : 2046 net assigned charge : 2.000009 assigned positive charge : 321.7015 centred at (gu) : 93.11538 93.00580 91.76430 assigned negative charge : -319.7019 centred at (gu) : 92.86245 93.22151 92.69028 start vw surface at 0.1000000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 183875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19357 grid for indexing accessible points = 1.400000 m= 94912 mr = 133813 m= 39556 mr = 77637 m= 12028 mr = 32253 m= 2538 mr = 9056 m= 277 mr = 1764 m= 10 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 78538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 16368 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) : 2.135787 object centre at (A) : 42.93600 38.80700 29.61250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3624058 -0.8627166 midg,1,midg; midg,igrid,midg 0.1137761 -0.1626463 1,midg,midg; igrid,midg,midg -0.3006482 -0.5249652 gauss-seidel spectral radius is 0.9993191 estimated iterations to convergence 302 setup time was (sec) 2.490000 now iterating at: 03:14:24 rms-change max change #iterations 10.52107 364.6355 at 10iterations 6.240712 132.0219 at 20iterations 3.691998 66.79827 at 30iterations 2.184634 43.62739 at 40iterations 1.290761 23.36748 at 50iterations 0.7630616 17.57545 at 60iterations 0.4488360 7.962190 at 70iterations 0.2653598 4.596406 at 80iterations 0.1559600 2.703846 at 90iterations 9.1563895E-02 1.540306 at 100iterations 5.3921025E-02 0.9262753 at 110iterations 3.1662237E-02 0.5448647 at 120iterations 1.8681791E-02 0.2861090 at 130iterations 1.0960931E-02 0.1806288 at 140iterations 6.4503918E-03 0.1101093 at 150iterations 3.7977591E-03 6.0475349E-02 at 160iterations 2.2410285E-03 3.8484097E-02 at 170iterations 1.3243320E-03 2.3254395E-02 at 180iterations finished qdiffx linear iterations at : 03:14:42 total time elapsed so far: 21.05000 # loops : 180 mean,max change (kT/e) : 1.3243320E-03 2.3254395E-02 energy calculations done at 21.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.21000 DelPhi exited at 03:14:43 21.219u 0.523s 0:22.08 98.4% 0+0k 0+0io 0pf+0w