Sun Oct 9 02:57:14 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 02:57:14 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4563 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.4493985 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): -2.407000 76.81001 ymin,ymax (A): 0.8160001 67.06200 zmin,zma (A): 164.8370 225.3710 x,y,z range (A): 79.21700 66.24599 60.53398 scale (grids/A): 0.4493985 object centre (A): 37.20150 33.93900 195.1040 number of atom coordinates read : 4563 total number of charged atoms : 4329 net assigned charge : 19.00001 assigned positive charge : 667.2070 centred at (gu) : 85.94629 91.08372 88.96246 assigned negative charge : -648.2117 centred at (gu) : 85.89061 91.03300 88.98571 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5463 nv = 96 ne = 84 npr = 93677 no. pairs analyzed = 93677 no. exposed pairs = 5690 no. arc points = 39060 no. surface atoms = 1935 nbur = 2628 mkacc time = 0.1600000 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 = 1.876000 m= 142 mr = 2643 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3000000 number of dielectric boundary points 2960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3347 ## 646 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0015142E-11 6.9479140E-12 midg,1,midg; midg,igrid,midg 4.5097645E-12 2.4695324E-11 1,midg,midg; igrid,midg,midg 1.7164742E-11 5.7989607E-12 gauss-seidel spectral radius is 0.9747151 estimated iterations to convergence 52 setup time was (sec) 0.4800000 now iterating at: 02:57:15 rms-change max change #iterations 3.4243606E-02 5.619694 at 10iterations 2.6210118E-03 0.4621449 at 20iterations 4.2610380E-04 6.8016052E-02 at 30iterations 7.8057907E-05 1.2165070E-02 at 40iterations 1.4428038E-05 2.2239685E-03 at 50iterations finished qdiffx linear iterations at : 02:57:18 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.4428038E-05 2.2239685E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 02:57:18 3.576u 0.190s 0:04.03 93.3% 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 02:57:18 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4563 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.348195 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): -2.407000 76.81001 ymin,ymax (A): 0.8160001 67.06200 zmin,zma (A): 164.8370 225.3710 x,y,z range (A): 79.21700 66.24599 60.53398 scale (grids/A): 1.348195 object centre (A): 37.20150 33.93900 195.1040 number of atom coordinates read : 4563 total number of charged atoms : 4329 net assigned charge : 19.00001 assigned positive charge : 667.2070 centred at (gu) : 77.83713 93.24948 86.88587 assigned negative charge : -648.2117 centred at (gu) : 77.67112 93.09875 86.95705 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 64156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39060 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 15300 mr = 42866 m= 808 mr = 9281 m= 7 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1170 time to turn everything in is 0.3400000 number of dielectric boundary points 27934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 609 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 30883 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) : 0.4493985 object centre at (A) : 37.20150 33.93900 195.1040 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0928922E-03 1.0654259E-03 midg,1,midg; midg,igrid,midg 2.4222266E-03 3.7119461E-03 1,midg,midg; igrid,midg,midg 2.4476543E-02 3.6021241E-03 gauss-seidel spectral radius is 0.9974318 estimated iterations to convergence 157 setup time was (sec) 0.5500000 now iterating at: 02:57:19 rms-change max change #iterations 2.634337 125.8011 at 10iterations 0.9253280 36.60540 at 20iterations 0.3296241 12.63533 at 30iterations 0.1166077 5.269428 at 40iterations 4.1699629E-02 1.729742 at 50iterations 1.4942904E-02 0.5862427 at 60iterations 5.4970426E-03 0.2166595 at 70iterations 2.1125018E-03 8.4587097E-02 at 80iterations 8.6884369E-04 3.4679413E-02 at 90iterations 3.9147257E-04 1.3502121E-02 at 100iterations 1.9348320E-04 6.6890717E-03 at 110iterations 1.0115381E-04 3.4046173E-03 at 120iterations finished qdiffx linear iterations at : 02:57:26 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.0115381E-04 3.4046173E-03 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 02:57:26 7.628u 0.197s 0:08.13 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 02:57:26 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4563 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.022293 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): -2.407000 76.81001 ymin,ymax (A): 0.8160001 67.06200 zmin,zma (A): 164.8370 225.3710 x,y,z range (A): 79.21700 66.24599 60.53398 scale (grids/A): 2.022293 object centre (A): 37.20150 33.93900 195.1040 number of atom coordinates read : 4563 total number of charged atoms : 4329 net assigned charge : 19.00001 assigned positive charge : 667.2070 centred at (gu) : 71.75523 94.87399 85.32837 assigned negative charge : -648.2117 centred at (gu) : 71.50674 94.64801 85.43546 start vw surface at 0.1200000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 150108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39060 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 58659 mr = 106285 m= 11410 mr = 43856 m= 1014 mr = 7458 m= 8 mr = 410 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 4032 time to turn everything in is 0.7700000 number of dielectric boundary points 63190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 34301 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) : 1.348195 object centre at (A) : 37.20150 33.93900 195.1040 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8968689E-02 1.5694696E-02 midg,1,midg; midg,igrid,midg 5.1421136E-02 7.7193528E-02 1,midg,midg; igrid,midg,midg 0.5737879 4.1179899E-02 gauss-seidel spectral radius is 0.9989156 estimated iterations to convergence 240 setup time was (sec) 1.010000 now iterating at: 02:57:27 rms-change max change #iterations 7.765752 253.4478 at 10iterations 4.078020 108.2985 at 20iterations 2.135702 54.03889 at 30iterations 1.110685 25.73483 at 40iterations 0.5752636 13.10641 at 50iterations 0.2979787 6.868469 at 60iterations 0.1534751 3.557390 at 70iterations 7.8854300E-02 1.776325 at 80iterations 4.0577866E-02 0.9145622 at 90iterations 2.0837992E-02 0.4813013 at 100iterations 1.0707982E-02 0.2685184 at 110iterations 5.5210423E-03 0.1350708 at 120iterations 2.8458564E-03 6.6219330E-02 at 130iterations 1.4691099E-03 3.1851292E-02 at 140iterations 7.6162047E-04 1.7753601E-02 at 150iterations 4.0201354E-04 8.7084770E-03 at 160iterations 2.1468749E-04 4.8980713E-03 at 170iterations 1.1696069E-04 2.5329590E-03 at 180iterations finished qdiffx linear iterations at : 02:57:38 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 1.1696069E-04 2.5329590E-03 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 02:57:39 12.159u 0.181s 0:12.60 97.8% 0+0k 0+0io 0pf+0w