Sun Oct 9 14:16:46 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 14:16:46 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 = 2646 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: 0.5549234 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): -2.813000 49.22800 ymin,ymax (A): -8.663000 38.79800 zmin,zma (A): -16.15000 48.00300 x,y,z range (A): 52.04100 47.46100 64.15300 scale (grids/A): 0.5549234 object centre (A): 23.20750 15.06750 15.92650 number of atom coordinates read : 2646 total number of charged atoms : 2507 net assigned charge : 4.500009 assigned positive charge : 399.5934 centred at (gu) : 90.54546 90.60019 88.83852 assigned negative charge : -395.0945 centred at (gu) : 90.39764 90.47124 88.93301 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5324 nv = 96 ne = 84 npr = 52472 no. pairs analyzed = 52472 no. exposed pairs = 3414 no. arc points = 23601 no. surface atoms = 1153 nbur = 1493 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 208 mr = 2714 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2433 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6863 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5138689E-09 -3.0515715E-10 midg,1,midg; midg,igrid,midg -6.0280475E-10 1.6370796E-09 1,midg,midg; igrid,midg,midg -7.5119472E-10 1.7864660E-09 gauss-seidel spectral radius is 0.9832258 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 14:16:47 rms-change max change #iterations 7.4956760E-02 13.77356 at 10iterations 5.1648850E-03 0.9499044 at 20iterations 3.9272822E-04 7.4525833E-02 at 30iterations 6.1308558E-05 1.5718460E-02 at 40iterations 1.7183995E-05 4.6520233E-03 at 50iterations finished qdiffx linear iterations at : 14:16:49 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.7183995E-05 4.6520233E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:16:50 3.391u 0.189s 0:03.86 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 14:16:50 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 = 2646 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: 1.664770 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): -2.813000 49.22800 ymin,ymax (A): -8.663000 38.79800 zmin,zma (A): -16.15000 48.00300 x,y,z range (A): 52.04100 47.46100 64.15300 scale (grids/A): 1.664770 object centre (A): 23.20750 15.06750 15.92650 number of atom coordinates read : 2646 total number of charged atoms : 2507 net assigned charge : 4.500009 assigned positive charge : 399.5934 centred at (gu) : 91.63564 91.79961 86.51475 assigned negative charge : -395.0945 centred at (gu) : 91.19254 91.41355 86.79876 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23601 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18412 mr = 39461 m= 1841 mr = 12491 m= 43 mr = 860 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 26079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19275 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) : 0.5549234 object centre at (A) : 23.20750 15.06750 15.92650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6181299E-02 5.5487114E-03 midg,1,midg; midg,igrid,midg -1.6452357E-03 5.1570912E-03 1,midg,midg; igrid,midg,midg -2.1375677E-02 -1.0666845E-03 gauss-seidel spectral radius is 0.9982232 estimated iterations to convergence 188 setup time was (sec) 0.5400000 now iterating at: 14:16:51 rms-change max change #iterations 3.180036 154.9069 at 10iterations 1.338656 49.49866 at 20iterations 0.5608292 25.28629 at 30iterations 0.2365729 8.862618 at 40iterations 9.9750616E-02 3.610306 at 50iterations 4.1960284E-02 1.737537 at 60iterations 1.7628318E-02 0.6705902 at 70iterations 7.4387733E-03 0.3262463 at 80iterations 3.1389515E-03 0.1213493 at 90iterations 1.3266341E-03 5.6160927E-02 at 100iterations 5.6072936E-04 1.9527435E-02 at 110iterations 2.3826897E-04 8.9721680E-03 at 120iterations finished qdiffx linear iterations at : 14:16:59 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 2.3826897E-04 8.9721680E-03 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 14:16:59 8.454u 0.238s 0:09.04 96.0% 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 14:16:59 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 = 2646 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: 2.497155 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): -2.813000 49.22800 ymin,ymax (A): -8.663000 38.79800 zmin,zma (A): -16.15000 48.00300 x,y,z range (A): 52.04100 47.46100 64.15300 scale (grids/A): 2.497155 object centre (A): 23.20750 15.06750 15.92650 number of atom coordinates read : 2646 total number of charged atoms : 2507 net assigned charge : 4.500009 assigned positive charge : 399.5934 centred at (gu) : 92.45329 92.69946 84.77206 assigned negative charge : -395.0945 centred at (gu) : 91.78867 92.12020 85.19798 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 136076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23601 grid for indexing accessible points = 1.400000 m= 63531 mr = 96722 m= 17760 mr = 49822 m= 2776 mr = 13090 m= 209 mr = 1825 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 58819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20034 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) : 1.664770 object centre at (A) : 23.20750 15.06750 15.92650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7147952 0.1031752 midg,1,midg; midg,igrid,midg -2.0024063E-02 1.4792759E-02 1,midg,midg; igrid,midg,midg -0.3536392 -3.8200714E-02 gauss-seidel spectral radius is 0.9991409 estimated iterations to convergence 269 setup time was (sec) 1.010000 now iterating at: 14:17:00 rms-change max change #iterations 8.350143 291.0324 at 10iterations 4.772277 125.5565 at 20iterations 2.697793 72.79036 at 30iterations 1.514982 40.35860 at 40iterations 0.8456506 22.40220 at 50iterations 0.4714627 11.25970 at 60iterations 0.2629755 5.876579 at 70iterations 0.1461493 3.320818 at 80iterations 8.0818251E-02 1.688481 at 90iterations 4.4630911E-02 0.9613738 at 100iterations 2.4651205E-02 0.5488291 at 110iterations 1.3613668E-02 0.2959747 at 120iterations 7.5362502E-03 0.1682739 at 130iterations 4.1547907E-03 9.8365784E-02 at 140iterations 2.3019551E-03 4.9041748E-02 at 150iterations 1.2754770E-03 2.8102875E-02 at 160iterations 7.0945889E-04 1.5716553E-02 at 170iterations 3.9889419E-04 9.7017288E-03 at 180iterations finished qdiffx linear iterations at : 14:17:13 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 3.9889419E-04 9.7017288E-03 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.41000 DelPhi exited at 14:17:13 13.408u 0.253s 0:14.09 96.8% 0+0k 0+0io 0pf+0w