Tue Oct 11 08:09:07 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 08:09:07 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 = 1326 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7060970 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): -39.93300 7.922000 ymin,ymax (A): -61.62600 -11.20800 zmin,zma (A): -33.63600 9.102000 x,y,z range (A): 47.85500 50.41800 42.73800 scale (grids/A): 0.7060970 object centre (A): -16.00550 -36.41700 -12.26700 number of atom coordinates read : 1326 total number of charged atoms : 1193 net assigned charge : -0.4999950 assigned positive charge : 190.8032 centred at (gu) : 88.26317 90.17056 88.65070 assigned negative charge : -191.3031 centred at (gu) : 88.28783 90.12397 88.74923 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4617 nv = 96 ne = 84 npr = 25230 no. pairs analyzed = 25230 no. exposed pairs = 2063 no. arc points = 15186 no. surface atoms = 679 nbur = 647 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 2024 m= 0 mr = 21 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1230 ## 115 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 4851 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1494249E-08 -2.5904578E-08 midg,1,midg; midg,igrid,midg -1.7751418E-08 9.2504120E-09 1,midg,midg; igrid,midg,midg 3.7506096E-09 -8.4902840E-09 gauss-seidel spectral radius is 0.9894890 estimated iterations to convergence 79 setup time was (sec) 0.4900000 now iterating at: 08:09:08 rms-change max change #iterations 0.1521447 29.98838 at 10iterations 1.7998377E-02 3.789166 at 20iterations 2.1457383E-03 0.4368639 at 30iterations 2.5459638E-04 4.6722412E-02 at 40iterations 3.0268884E-05 4.6920776E-03 at 50iterations finished qdiffx linear iterations at : 08:09:11 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 3.0268884E-05 4.6920776E-03 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.920000 DelPhi exited at 08:09:12 3.919u 0.263s 0:04.73 88.1% 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 08:09:12 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 = 1326 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.118291 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): -39.93300 7.922000 ymin,ymax (A): -61.62600 -11.20800 zmin,zma (A): -33.63600 9.102000 x,y,z range (A): 47.85500 50.41800 42.73800 scale (grids/A): 2.118291 object centre (A): -16.00550 -36.41700 -12.26700 number of atom coordinates read : 1326 total number of charged atoms : 1193 net assigned charge : -0.4999950 assigned positive charge : 190.8032 centred at (gu) : 84.78961 90.51186 85.95216 assigned negative charge : -191.3031 centred at (gu) : 84.86375 90.37190 86.24775 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 47493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15186 grid for indexing accessible points = 1.400000 m= 16371 mr = 28116 m= 3155 mr = 10949 m= 276 mr = 1792 m= 16 mr = 83 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 26368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 9483 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) : 0.7060970 object centre at (A) : -16.00550 -36.41700 -12.26700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4963237E-04 -1.2502549E-02 midg,1,midg; midg,igrid,midg -1.1752939E-02 -1.2870693E-03 1,midg,midg; igrid,midg,midg -1.5637286E-02 3.1879877E-03 gauss-seidel spectral radius is 0.9987664 estimated iterations to convergence 225 setup time was (sec) 0.7700000 now iterating at: 08:09:13 rms-change max change #iterations 3.532107 189.8283 at 10iterations 1.701254 69.69404 at 20iterations 0.8208131 33.52657 at 30iterations 0.3966752 15.74150 at 40iterations 0.1918000 7.990894 at 50iterations 9.2119031E-02 3.347657 at 60iterations 4.4624813E-02 1.701271 at 70iterations 2.1535560E-02 0.8464661 at 80iterations 1.0381179E-02 0.4054217 at 90iterations 5.0258962E-03 0.1847534 at 100iterations 2.4262147E-03 9.7138524E-02 at 110iterations 1.1780101E-03 4.9430847E-02 at 120iterations finished qdiffx linear iterations at : 08:09:21 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 1.1780101E-03 4.9430847E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 08:09:22 9.286u 0.328s 0:10.55 90.9% 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 08:09:22 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 = 1326 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.177436 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): -39.93300 7.922000 ymin,ymax (A): -61.62600 -11.20800 zmin,zma (A): -33.63600 9.102000 x,y,z range (A): 47.85500 50.41800 42.73800 scale (grids/A): 3.177436 object centre (A): -16.00550 -36.41700 -12.26700 number of atom coordinates read : 1326 total number of charged atoms : 1193 net assigned charge : -0.4999950 assigned positive charge : 190.8032 centred at (gu) : 82.18444 90.76785 83.92831 assigned negative charge : -191.3031 centred at (gu) : 82.29559 90.55790 84.37170 start vw surface at 0.1300000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 109184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15186 grid for indexing accessible points = 1.400000 m= 50502 mr = 68873 m= 19945 mr = 38393 m= 5700 mr = 15121 m= 1015 mr = 3923 m= 128 mr = 582 m= 13 mr = 71 m= 0 mr = 5 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.500000 number of dielectric boundary points 59519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 9544 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) : 2.118291 object centre at (A) : -16.00550 -36.41700 -12.26700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7851783E-02 -8.2676999E-02 midg,1,midg; midg,igrid,midg -7.4435649E-03 -9.9026393E-03 1,midg,midg; igrid,midg,midg -0.2353711 4.8144612E-02 gauss-seidel spectral radius is 0.9992888 estimated iterations to convergence 296 setup time was (sec) 1.820000 now iterating at: 08:09:25 rms-change max change #iterations 8.190001 354.4214 at 10iterations 4.864483 140.1935 at 20iterations 2.865454 74.14156 at 30iterations 1.674517 40.08560 at 40iterations 0.9765999 21.14787 at 50iterations 0.5697995 14.58247 at 60iterations 0.3316184 8.097990 at 70iterations 0.1919487 4.322681 at 80iterations 0.1115973 2.229658 at 90iterations 6.4607449E-02 1.556716 at 100iterations 3.7500396E-02 0.7621613 at 110iterations 2.1700617E-02 0.5284996 at 120iterations 1.2584133E-02 0.2560349 at 130iterations 7.2758119E-03 0.1480429 at 140iterations 4.2288359E-03 9.3488216E-02 at 150iterations 2.4513111E-03 5.0617218E-02 at 160iterations 1.4182804E-03 2.8880119E-02 at 170iterations 8.2037924E-04 1.7391205E-02 at 180iterations finished qdiffx linear iterations at : 08:09:38 total time elapsed so far: 15.12000 # loops : 180 mean,max change (kT/e) : 8.2037924E-04 1.7391205E-02 energy calculations done at 15.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.30000 DelPhi exited at 08:09:39 15.305u 0.582s 0:16.52 96.1% 0+0k 0+0io 0pf+0w