Mon Oct 10 22:22:09 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 Mon Oct 10 2011 at 22:22:09 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 = 2637 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5881964 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): 14.41700 74.94100 ymin,ymax (A): -11.92200 43.76700 zmin,zma (A): -7.993000 35.21200 x,y,z range (A): 60.52400 55.68900 43.20500 scale (grids/A): 0.5881964 object centre (A): 44.67900 15.92250 13.60950 number of atom coordinates read : 2637 total number of charged atoms : 2495 net assigned charge : 3.500016 assigned positive charge : 395.3587 centred at (gu) : 89.29149 90.18261 89.82742 assigned negative charge : -391.8594 centred at (gu) : 89.52721 90.34725 90.01706 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 5922 nv = 96 ne = 84 npr = 54000 no. pairs analyzed = 54000 no. exposed pairs = 3097 no. arc points = 21450 no. surface atoms = 1052 nbur = 1585 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 = 1.456000 m= 244 mr = 3306 m= 0 mr = 12 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.4100000 number of dielectric boundary points 2848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2208 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 7547 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9234306E-09 -3.7824490E-09 midg,1,midg; midg,igrid,midg 4.8694604E-09 -3.4265639E-09 1,midg,midg; igrid,midg,midg 8.0315381E-09 -4.3713997E-09 gauss-seidel spectral radius is 0.9850453 estimated iterations to convergence 67 setup time was (sec) 0.6900000 now iterating at: 22:22:10 rms-change max change #iterations 9.8280728E-02 15.49675 at 10iterations 8.9425156E-03 1.543800 at 20iterations 1.0678733E-03 0.2485580 at 30iterations 2.4451417E-04 6.3465118E-02 at 40iterations 6.2447725E-05 1.6635895E-02 at 50iterations finished qdiffx linear iterations at : 22:22:13 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 6.2447725E-05 1.6635895E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 22:22:14 4.052u 0.144s 0:04.57 91.6% 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 Mon Oct 10 2011 at 22:22:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.764589 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): 14.41700 74.94100 ymin,ymax (A): -11.92200 43.76700 zmin,zma (A): -7.993000 35.21200 x,y,z range (A): 60.52400 55.68900 43.20500 scale (grids/A): 1.764589 object centre (A): 44.67900 15.92250 13.60950 number of atom coordinates read : 2637 total number of charged atoms : 2495 net assigned charge : 3.500016 assigned positive charge : 395.3587 centred at (gu) : 87.87411 90.54738 89.48158 assigned negative charge : -391.8594 centred at (gu) : 88.58141 91.04167 90.05094 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 65514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21450 grid for indexing accessible points = 1.400000 m= 20948 mr = 46057 m= 2515 mr = 15179 m= 65 mr = 1532 m= 0 mr = 11 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1881 time to turn everything in is 0.6300000 number of dielectric boundary points 26263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19394 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) : 0.5881964 object centre at (A) : 44.67900 15.92250 13.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1287452E-02 -1.2268926E-03 midg,1,midg; midg,igrid,midg 2.5967764E-02 -2.0064538E-02 1,midg,midg; igrid,midg,midg -3.6771155E-03 -4.9634166E-02 gauss-seidel spectral radius is 0.9984121 estimated iterations to convergence 199 setup time was (sec) 0.9900000 now iterating at: 22:22:15 rms-change max change #iterations 3.662528 151.9091 at 10iterations 1.610255 58.53853 at 20iterations 0.7128116 26.80606 at 30iterations 0.3130570 11.62334 at 40iterations 0.1394310 4.638381 at 50iterations 6.1591052E-02 2.218980 at 60iterations 2.7224548E-02 1.020386 at 70iterations 1.2065984E-02 0.4205751 at 80iterations 5.3889537E-03 0.2031097 at 90iterations 2.4278022E-03 9.1186523E-02 at 100iterations 1.1208275E-03 4.4269562E-02 at 110iterations 5.3143391E-04 2.2507668E-02 at 120iterations finished qdiffx linear iterations at : 22:22:23 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 5.3143391E-04 2.2507668E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 22:22:24 9.629u 0.265s 0:10.43 94.7% 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 Mon Oct 10 2011 at 22:22:24 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 = 2637 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 2.646884 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): 14.41700 74.94100 ymin,ymax (A): -11.92200 43.76700 zmin,zma (A): -7.993000 35.21200 x,y,z range (A): 60.52400 55.68900 43.20500 scale (grids/A): 2.646884 object centre (A): 44.67900 15.92250 13.60950 number of atom coordinates read : 2637 total number of charged atoms : 2495 net assigned charge : 3.500016 assigned positive charge : 395.3587 centred at (gu) : 86.81090 90.82101 89.22234 assigned negative charge : -391.8594 centred at (gu) : 87.87212 91.56242 90.07633 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 151967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21450 grid for indexing accessible points = 1.400000 m= 71843 mr = 111833 m= 21939 mr = 58527 m= 4273 mr = 17437 m= 338 mr = 3219 m= 3 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 6528 time to turn everything in is 1.460000 number of dielectric boundary points 59165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 19955 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) : 1.764589 object centre at (A) : 44.67900 15.92250 13.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2371715 8.6247884E-03 midg,1,midg; midg,igrid,midg 0.3824844 -0.5807720 1,midg,midg; igrid,midg,midg -0.1185391 -0.6878099 gauss-seidel spectral radius is 0.9991911 estimated iterations to convergence 278 setup time was (sec) 1.850000 now iterating at: 22:22:26 rms-change max change #iterations 8.872655 277.7962 at 10iterations 5.016011 110.4267 at 20iterations 2.824281 61.06183 at 30iterations 1.590915 34.95448 at 40iterations 0.8935317 18.05157 at 50iterations 0.5001287 11.43072 at 60iterations 0.2804309 6.727499 at 70iterations 0.1569837 3.187922 at 80iterations 8.8061996E-02 1.803566 at 90iterations 4.9322117E-02 0.9447079 at 100iterations 2.7662549E-02 0.5318527 at 110iterations 1.5512655E-02 0.2930841 at 120iterations 8.7283114E-03 0.1781464 at 130iterations 4.9075792E-03 0.1136017 at 140iterations 2.7849714E-03 6.2435150E-02 at 150iterations 1.5929650E-03 3.9684296E-02 at 160iterations 9.2832954E-04 2.1869659E-02 at 170iterations 5.5230560E-04 1.5605927E-02 at 180iterations finished qdiffx linear iterations at : 22:22:39 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 5.5230560E-04 1.5605927E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.34000 DelPhi exited at 22:22:40 15.343u 0.274s 0:15.99 97.6% 0+0k 0+0io 0pf+0w