Sat Oct 8 14:48:30 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 14:48:30 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: NAP 500 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: 0.6407257 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): -12.20900 43.35300 ymin,ymax (A): -23.86900 22.76600 zmin,zma (A): -7.726000 47.66900 x,y,z range (A): 55.56200 46.63500 55.39500 scale (grids/A): 0.6407257 object centre (A): 15.57200 -0.5515003 19.97150 number of atom coordinates read : 2975 total number of charged atoms : 2830 net assigned charge : 1.228008 assigned positive charge : 445.4236 centred at (gu) : 88.79015 89.97415 91.67451 assigned negative charge : -444.1964 centred at (gu) : 88.71094 89.82452 91.66976 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8078 nv = 96 ne = 84 npr = 61726 no. pairs analyzed = 61726 no. exposed pairs = 3410 no. arc points = 24122 no. surface atoms = 1168 nbur = 1807 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4653 m= 0 mr = 56 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2352 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9808 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5405028E-10 3.7390708E-09 midg,1,midg; midg,igrid,midg -1.8742396E-08 2.1808120E-08 1,midg,midg; igrid,midg,midg -1.1581935E-08 9.7339106E-09 gauss-seidel spectral radius is 0.9874099 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 14:48:31 rms-change max change #iterations 0.1600264 19.12174 at 10iterations 1.5923901E-02 1.966278 at 20iterations 1.6560119E-03 0.2291861 at 30iterations 2.0716058E-04 2.9674530E-02 at 40iterations 3.3892604E-05 4.5280457E-03 at 50iterations finished qdiffx linear iterations at : 14:48:33 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 3.3892604E-05 4.5280457E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 14:48:34 3.129u 0.154s 0:03.68 88.8% 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 14:48:34 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.922177 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): -12.20900 43.35300 ymin,ymax (A): -23.86900 22.76600 zmin,zma (A): -7.726000 47.66900 x,y,z range (A): 55.56200 46.63500 55.39500 scale (grids/A): 1.922177 object centre (A): 15.57200 -0.5515003 19.97150 number of atom coordinates read : 2975 total number of charged atoms : 2830 net assigned charge : 1.228008 assigned positive charge : 445.4236 centred at (gu) : 86.36964 89.92188 95.02284 assigned negative charge : -444.1964 centred at (gu) : 86.13274 89.47330 95.00899 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 88465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24122 grid for indexing accessible points = 1.400000 m= 31897 mr = 63402 m= 4754 mr = 23932 m= 321 mr = 2958 m= 1 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.5800000 number of dielectric boundary points 35009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22291 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) : 0.6407257 object centre at (A) : 15.57200 -0.5515003 19.97150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3525188E-03 1.6980695E-02 midg,1,midg; midg,igrid,midg -5.1832353E-03 3.0119915E-02 1,midg,midg; igrid,midg,midg -4.5735534E-02 1.3672280E-02 gauss-seidel spectral radius is 0.9986914 estimated iterations to convergence 219 setup time was (sec) 0.8400000 now iterating at: 14:48:35 rms-change max change #iterations 4.649280 197.6451 at 10iterations 2.222282 64.51339 at 20iterations 1.058776 34.86051 at 30iterations 0.5052364 14.63532 at 40iterations 0.2400020 7.261757 at 50iterations 0.1146186 3.535141 at 60iterations 5.4426678E-02 1.450101 at 70iterations 2.5977690E-02 0.7107296 at 80iterations 1.2369446E-02 0.3486605 at 90iterations 5.9084012E-03 0.1565514 at 100iterations 2.8142952E-03 8.4047318E-02 at 110iterations 1.3425805E-03 4.2182922E-02 at 120iterations finished qdiffx linear iterations at : 14:48:41 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 1.3425805E-03 4.2182922E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 14:48:41 7.002u 0.187s 0:07.57 94.8% 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 14:48:41 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: NAP 500 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: 2.883265 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): -12.20900 43.35300 ymin,ymax (A): -23.86900 22.76600 zmin,zma (A): -7.726000 47.66900 x,y,z range (A): 55.56200 46.63500 55.39500 scale (grids/A): 2.883265 object centre (A): 15.57200 -0.5515003 19.97150 number of atom coordinates read : 2975 total number of charged atoms : 2830 net assigned charge : 1.228008 assigned positive charge : 445.4236 centred at (gu) : 84.55445 89.88262 97.53410 assigned negative charge : -444.1964 centred at (gu) : 84.19903 89.20986 97.51350 start vw surface at 0.1800000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 205198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24122 grid for indexing accessible points = 1.400000 m= 103842 mr = 153448 m= 36523 mr = 86470 m= 8550 mr = 29444 m= 1340 mr = 6348 m= 124 mr = 923 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 186 time to turn everything in is 1.520000 number of dielectric boundary points 78883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 22640 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) : 1.922177 object centre at (A) : 15.57200 -0.5515003 19.97150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1284126E-02 0.2905303 midg,1,midg; midg,igrid,midg -4.0309001E-02 0.3237902 1,midg,midg; igrid,midg,midg -0.4669645 0.1442532 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 1.800000 now iterating at: 14:48:43 rms-change max change #iterations 10.82706 478.0771 at 10iterations 6.351194 132.5534 at 20iterations 3.704955 68.11555 at 30iterations 2.156127 41.14975 at 40iterations 1.251046 24.84649 at 50iterations 0.7282416 14.80406 at 60iterations 0.4229323 7.393382 at 70iterations 0.2453365 4.811991 at 80iterations 0.1422070 2.588394 at 90iterations 8.2381971E-02 1.288685 at 100iterations 4.7744103E-02 0.8303604 at 110iterations 2.7679695E-02 0.4394665 at 120iterations 1.6029408E-02 0.2542801 at 130iterations 9.3044229E-03 0.1603870 at 140iterations 5.3792396E-03 8.6444855E-02 at 150iterations 3.1219441E-03 5.0013751E-02 at 160iterations 1.8259519E-03 3.1471252E-02 at 170iterations 1.0695311E-03 1.7305136E-02 at 180iterations finished qdiffx linear iterations at : 14:48:53 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 1.0695311E-03 1.7305136E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 14:48:53 11.614u 0.179s 0:12.12 97.1% 0+0k 0+0io 0pf+0w