Sun Oct 9 08:16:08 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 08:16:08 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 = 5073 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: 0.4905744 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): -31.98600 25.46900 ymin,ymax (A): -13.43100 59.13700 zmin,zma (A): -28.90100 36.81600 x,y,z range (A): 57.45500 72.56800 65.71700 scale (grids/A): 0.4905744 object centre (A): -3.258500 22.85300 3.957500 number of atom coordinates read : 5073 total number of charged atoms : 4908 net assigned charge : -0.9999963 assigned positive charge : 753.0505 centred at (gu) : 88.47552 89.89307 89.98058 assigned negative charge : -754.0555 centred at (gu) : 88.43947 89.81427 90.03220 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7622 nv = 96 ne = 84 npr = 102201 no. pairs analyzed = 102201 no. exposed pairs = 6428 no. arc points = 45162 no. surface atoms = 2164 nbur = 2909 mkacc time = 0.1700000 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 = 1.736000 m= 260 mr = 3807 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4245 ## 703 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10354 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2957961E-11 -6.2702010E-11 midg,1,midg; midg,igrid,midg -9.6890745E-11 8.0170114E-11 1,midg,midg; igrid,midg,midg -6.9412177E-11 2.3231353E-11 gauss-seidel spectral radius is 0.9787832 estimated iterations to convergence 57 setup time was (sec) 0.5200000 now iterating at: 08:16:09 rms-change max change #iterations 5.6802958E-02 10.08028 at 10iterations 3.1972483E-03 0.6854477 at 20iterations 4.3100750E-04 0.1140556 at 30iterations 1.1916093E-04 3.1452179E-02 at 40iterations 3.6266425E-05 9.0866089E-03 at 50iterations finished qdiffx linear iterations at : 08:16:12 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 3.6266425E-05 9.0866089E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 08:16:13 3.519u 0.170s 0:04.20 87.6% 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 Sun Oct 9 2011 at 08:16:13 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 = 5073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.471723 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): -31.98600 25.46900 ymin,ymax (A): -13.43100 59.13700 zmin,zma (A): -28.90100 36.81600 x,y,z range (A): 57.45500 72.56800 65.71700 scale (grids/A): 1.471723 object centre (A): -3.258500 22.85300 3.957500 number of atom coordinates read : 5073 total number of charged atoms : 4908 net assigned charge : -0.9999963 assigned positive charge : 753.0505 centred at (gu) : 85.42527 89.67780 89.94019 assigned negative charge : -754.0555 centred at (gu) : 85.31789 89.44239 90.09640 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 87394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45162 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 23547 mr = 59321 m= 1767 mr = 14932 m= 34 mr = 601 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 783 time to turn everything in is 0.4400000 number of dielectric boundary points 37888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 607 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 36306 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) : 0.4905744 object centre at (A) : -3.258500 22.85300 3.957500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8949577E-03 -3.8971142E-03 midg,1,midg; midg,igrid,midg 7.6354286E-03 1.9877378E-02 1,midg,midg; igrid,midg,midg -9.4290654E-04 -1.2662332E-03 gauss-seidel spectral radius is 0.9979708 estimated iterations to convergence 177 setup time was (sec) 0.6500000 now iterating at: 08:16:14 rms-change max change #iterations 3.554487 135.8129 at 10iterations 1.407301 46.04773 at 20iterations 0.5591332 19.11213 at 30iterations 0.2215665 7.601881 at 40iterations 8.8276207E-02 3.030979 at 50iterations 3.5077307E-02 1.254088 at 60iterations 1.3961809E-02 0.4767914 at 70iterations 5.5781635E-03 0.1792376 at 80iterations 2.2648231E-03 8.5834503E-02 at 90iterations 9.4253232E-04 3.3494949E-02 at 100iterations 4.1512016E-04 1.9958496E-02 at 110iterations 2.0248671E-04 9.3021393E-03 at 120iterations finished qdiffx linear iterations at : 08:16:21 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.0248671E-04 9.3021393E-03 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 08:16:21 7.811u 0.185s 0:08.29 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 08:16:21 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 = 5073 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: 2.207585 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): -31.98600 25.46900 ymin,ymax (A): -13.43100 59.13700 zmin,zma (A): -28.90100 36.81600 x,y,z range (A): 57.45500 72.56800 65.71700 scale (grids/A): 2.207585 object centre (A): -3.258500 22.85300 3.957500 number of atom coordinates read : 5073 total number of charged atoms : 4908 net assigned charge : -0.9999963 assigned positive charge : 753.0505 centred at (gu) : 83.13770 89.51624 89.91003 assigned negative charge : -754.0555 centred at (gu) : 82.97684 89.16366 90.14451 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 204150 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45162 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 86736 mr = 146411 m= 19328 mr = 66030 m= 2256 mr = 13162 m= 107 mr = 1285 m= 0 mr = 26 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 2655 time to turn everything in is 1.030000 number of dielectric boundary points 85663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 39098 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) : 1.471723 object centre at (A) : -3.258500 22.85300 3.957500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1910676 -5.7713776E-03 midg,1,midg; midg,igrid,midg 0.2264753 0.6663955 1,midg,midg; igrid,midg,midg 3.5050284E-02 -4.4764102E-02 gauss-seidel spectral radius is 0.9991332 estimated iterations to convergence 268 setup time was (sec) 1.280000 now iterating at: 08:16:23 rms-change max change #iterations 10.01882 287.2074 at 10iterations 5.735260 132.3705 at 20iterations 3.250602 68.79025 at 30iterations 1.835853 40.71210 at 40iterations 1.029862 21.93272 at 50iterations 0.5762318 13.59845 at 60iterations 0.3209598 6.778653 at 70iterations 0.1786530 3.288894 at 80iterations 9.9182345E-02 2.055393 at 90iterations 5.4975647E-02 1.117698 at 100iterations 3.0485732E-02 0.5892248 at 110iterations 1.6789814E-02 0.3181305 at 120iterations 9.2928018E-03 0.1821032 at 130iterations 5.1283371E-03 9.6954346E-02 at 140iterations 2.8273640E-03 5.2808762E-02 at 150iterations 1.5652227E-03 2.7515411E-02 at 160iterations 8.6471805E-04 1.6586304E-02 at 170iterations 4.7907198E-04 1.0272026E-02 at 180iterations finished qdiffx linear iterations at : 08:16:34 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 4.7907198E-04 1.0272026E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 08:16:35 12.929u 0.217s 0:13.51 97.1% 0+0k 0+0io 0pf+0w