Sat Oct 8 19:36:15 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 Sat Oct 8 2011 at 19:36:15 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6186033 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): -31.93900 17.55700 ymin,ymax (A): -23.43600 23.39300 zmin,zma (A): -12.35600 45.19300 x,y,z range (A): 49.49600 46.82900 57.54900 scale (grids/A): 0.6186033 object centre (A): -7.191001 -2.1499634E-02 16.41850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.68104 89.08849 89.50463 assigned negative charge : -388.8955 centred at (gu) : 88.56848 89.14332 89.39302 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6454 nv = 96 ne = 84 npr = 54800 no. pairs analyzed = 54800 no. exposed pairs = 3022 no. arc points = 21740 no. surface atoms = 1004 nbur = 1602 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3596 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 176 time to turn everything in is 0.3200000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0768504E-09 9.5111705E-09 midg,1,midg; midg,igrid,midg 8.6257748E-09 8.2339212E-11 1,midg,midg; igrid,midg,midg -5.0481592E-09 7.9876292E-09 gauss-seidel spectral radius is 0.9864640 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 19:36:16 rms-change max change #iterations 0.1261687 19.90578 at 10iterations 1.1495799E-02 1.990276 at 20iterations 1.0661578E-03 0.1572886 at 30iterations 9.8635392E-05 1.5251160E-02 at 40iterations 9.2745049E-06 1.2874603E-03 at 50iterations finished qdiffx linear iterations at : 19:36:20 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 9.2745049E-06 1.2874603E-03 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 19:36:20 4.698u 0.406s 0:05.38 94.6% 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 Sat Oct 8 2011 at 19:36:20 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.855810 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): -31.93900 17.55700 ymin,ymax (A): -23.43600 23.39300 zmin,zma (A): -12.35600 45.19300 x,y,z range (A): 49.49600 46.82900 57.54900 scale (grids/A): 1.855810 object centre (A): -7.191001 -2.1499634E-02 16.41850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 86.04304 87.26492 88.51343 assigned negative charge : -388.8955 centred at (gu) : 85.70497 87.42952 88.17898 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21740 grid for indexing accessible points = 1.400000 m= 24231 mr = 48909 m= 3470 mr = 18010 m= 177 mr = 2155 m= 0 mr = 57 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 7746 time to turn everything in is 0.5600000 number of dielectric boundary points 29058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19345 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) : 0.6186033 object centre at (A) : -7.191001 -2.1499634E-02 16.41850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3788810E-02 2.7400369E-02 midg,1,midg; midg,igrid,midg 1.3518984E-02 -7.8796607E-04 1,midg,midg; igrid,midg,midg -3.5382381E-03 3.6063164E-02 gauss-seidel spectral radius is 0.9985611 estimated iterations to convergence 209 setup time was (sec) 0.8500000 now iterating at: 19:36:21 rms-change max change #iterations 4.034399 145.2544 at 10iterations 1.844377 67.77583 at 20iterations 0.8463308 27.13469 at 30iterations 0.3879868 14.20282 at 40iterations 0.1785181 6.167093 at 50iterations 8.1978358E-02 2.732777 at 60iterations 3.7741143E-02 1.305429 at 70iterations 1.7343760E-02 0.5532150 at 80iterations 7.9660844E-03 0.2772369 at 90iterations 3.6447970E-03 0.1242762 at 100iterations 1.6747768E-03 5.3047180E-02 at 110iterations 7.6941244E-04 2.6848793E-02 at 120iterations finished qdiffx linear iterations at : 19:36:31 total time elapsed so far: 10.57000 # loops : 120 mean,max change (kT/e) : 7.6941244E-04 2.6848793E-02 energy calculations done at 10.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.74000 DelPhi exited at 19:36:32 10.749u 0.456s 0:11.47 97.5% 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 Sat Oct 8 2011 at 19:36:32 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.783715 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): -31.93900 17.55700 ymin,ymax (A): -23.43600 23.39300 zmin,zma (A): -12.35600 45.19300 x,y,z range (A): 49.49600 46.82900 57.54900 scale (grids/A): 2.783715 object centre (A): -7.191001 -2.1499634E-02 16.41850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 84.06435 85.89705 87.76981 assigned negative charge : -388.8955 centred at (gu) : 83.55745 86.14416 87.26840 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 162489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21740 grid for indexing accessible points = 1.400000 m= 80213 mr = 118377 m= 27411 mr = 65918 m= 6186 mr = 22146 m= 753 mr = 4718 m= 48 mr = 504 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 25929 time to turn everything in is 1.470000 number of dielectric boundary points 65415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 19725 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) : 1.855810 object centre at (A) : -7.191001 -2.1499634E-02 16.41850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1789750E-03 0.3382724 midg,1,midg; midg,igrid,midg 0.1494101 -6.3826465E-03 1,midg,midg; igrid,midg,midg -4.1924410E-02 0.4602330 gauss-seidel spectral radius is 0.9992327 estimated iterations to convergence 285 setup time was (sec) 1.800000 now iterating at: 19:36:34 rms-change max change #iterations 9.440546 290.3211 at 10iterations 5.417902 127.4817 at 20iterations 3.091328 64.32930 at 30iterations 1.765491 41.14370 at 40iterations 1.007706 19.76530 at 50iterations 0.5735538 11.20577 at 60iterations 0.3269525 6.498468 at 70iterations 0.1856782 3.698015 at 80iterations 0.1056738 1.950328 at 90iterations 6.0030382E-02 1.138235 at 100iterations 3.4094486E-02 0.6356926 at 110iterations 1.9413371E-02 0.3755836 at 120iterations 1.1030159E-02 0.1974394 at 130iterations 6.2708035E-03 0.1295853 at 140iterations 3.5647794E-03 7.0070267E-02 at 150iterations 2.0314651E-03 3.6059380E-02 at 160iterations 1.1546947E-03 2.1622181E-02 at 170iterations 6.5512111E-04 1.2245178E-02 at 180iterations finished qdiffx linear iterations at : 19:36:50 total time elapsed so far: 18.03000 # loops : 180 mean,max change (kT/e) : 6.5512111E-04 1.2245178E-02 energy calculations done at 18.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.21000 DelPhi exited at 19:36:51 18.212u 0.437s 0:18.93 98.4% 0+0k 0+0io 0pf+0w