Tue Oct 11 03:25:04 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+sph2.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 = amb2.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 03:25:04 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1163 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: 0.7447387 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): -6.875000 30.70000 ymin,ymax (A): 1.165000 40.62200 zmin,zma (A): -1.445000 46.35700 x,y,z range (A): 37.57500 39.45700 47.80200 scale (grids/A): 0.7447387 object centre (A): 11.91250 20.89350 22.45600 number of atom coordinates read : 1163 total number of charged atoms : 1052 net assigned charge : 5.500003 assigned positive charge : 174.5531 centred at (gu) : 89.32140 88.82890 88.31072 assigned negative charge : -169.0531 centred at (gu) : 89.03431 88.81395 88.34631 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4458 nv = 96 ne = 84 npr = 22390 no. pairs analyzed = 22390 no. exposed pairs = 1474 no. arc points = 10982 no. surface atoms = 501 nbur = 662 mkacc time = 3.0000001E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 256 mr = 2317 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 3.0000001E-02 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.1200000 number of dielectric boundary points 2356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 895 ## 94 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7573534E-07 6.4916520E-08 midg,1,midg; midg,igrid,midg 1.2259900E-07 9.4858798E-08 1,midg,midg; igrid,midg,midg -7.5408423E-08 2.4021753E-07 gauss-seidel spectral radius is 0.9905068 estimated iterations to convergence 83 setup time was (sec) 0.3100000 now iterating at: 03:25:04 rms-change max change #iterations 0.1789659 35.79699 at 10iterations 2.4364810E-02 4.058920 at 20iterations 3.2282893E-03 0.5669670 at 30iterations 4.3052444E-04 6.8874359E-02 at 40iterations 5.9259426E-05 1.1967659E-02 at 50iterations finished qdiffx linear iterations at : 03:25:07 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.9259426E-05 1.1967659E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 03:25:08 3.321u 0.160s 0:03.80 91.5% 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 03:25:08 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1163 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.234216 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): -6.875000 30.70000 ymin,ymax (A): 1.165000 40.62200 zmin,zma (A): -1.445000 46.35700 x,y,z range (A): 37.57500 39.45700 47.80200 scale (grids/A): 2.234216 object centre (A): 11.91250 20.89350 22.45600 number of atom coordinates read : 1163 total number of charged atoms : 1052 net assigned charge : 5.500003 assigned positive charge : 174.5531 centred at (gu) : 87.96433 86.48669 84.93228 assigned negative charge : -169.0531 centred at (gu) : 87.10312 86.44209 85.03914 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 46060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10982 grid for indexing accessible points = 1.400000 m= 17508 mr = 30079 m= 3405 mr = 13111 m= 342 mr = 2330 m= 16 mr = 202 m= 0 mr = 7 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 865 time to turn everything in is 0.2500000 number of dielectric boundary points 21602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8392 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) : 0.7447387 object centre at (A) : 11.91250 20.89350 22.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0619869E-02 1.4462175E-02 midg,1,midg; midg,igrid,midg 4.1179653E-02 3.0086247E-02 1,midg,midg; igrid,midg,midg -2.4891663E-02 3.7080355E-02 gauss-seidel spectral radius is 0.9988452 estimated iterations to convergence 233 setup time was (sec) 0.4600000 now iterating at: 03:25:08 rms-change max change #iterations 3.628279 207.0397 at 10iterations 1.803650 73.64688 at 20iterations 0.8956373 36.22712 at 30iterations 0.4462551 18.78909 at 40iterations 0.2211961 9.018811 at 50iterations 0.1097691 4.444336 at 60iterations 5.4426398E-02 1.966285 at 70iterations 2.7140027E-02 1.028534 at 80iterations 1.3374537E-02 0.5016289 at 90iterations 6.6501023E-03 0.2528696 at 100iterations 3.2979667E-03 0.1272087 at 110iterations 1.6413498E-03 6.1603546E-02 at 120iterations finished qdiffx linear iterations at : 03:25:15 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.6413498E-03 6.1603546E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 03:25:16 7.595u 0.201s 0:08.42 92.5% 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 03:25:16 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1163 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.351324 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): -6.875000 30.70000 ymin,ymax (A): 1.165000 40.62200 zmin,zma (A): -1.445000 46.35700 x,y,z range (A): 37.57500 39.45700 47.80200 scale (grids/A): 3.351324 object centre (A): 11.91250 20.89350 22.45600 number of atom coordinates read : 1163 total number of charged atoms : 1052 net assigned charge : 5.500003 assigned positive charge : 174.5531 centred at (gu) : 86.94646 84.73006 82.39844 assigned negative charge : -169.0531 centred at (gu) : 85.65472 84.66314 82.55878 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 106269 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10982 grid for indexing accessible points = 1.400000 m= 53644 mr = 72890 m= 22282 mr = 43824 m= 6438 mr = 18387 m= 1351 mr = 5093 m= 215 mr = 1052 m= 23 mr = 171 m= 0 mr = 19 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2751 time to turn everything in is 0.7600000 number of dielectric boundary points 48786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 8416 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) : 2.234216 object centre at (A) : 11.91250 20.89350 22.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3862549 0.1433741 midg,1,midg; midg,igrid,midg 0.3561259 0.2627834 1,midg,midg; igrid,midg,midg -0.1950209 0.2566882 gauss-seidel spectral radius is 0.9992924 estimated iterations to convergence 297 setup time was (sec) 0.9800000 now iterating at: 03:25:17 rms-change max change #iterations 7.934581 309.1487 at 10iterations 4.621547 126.7657 at 20iterations 2.679702 64.52107 at 30iterations 1.547438 33.10403 at 40iterations 0.8994979 19.33382 at 50iterations 0.5208617 11.22674 at 60iterations 0.3008113 6.201557 at 70iterations 0.1745204 3.838699 at 80iterations 0.1012845 2.176811 at 90iterations 5.8752328E-02 1.378922 at 100iterations 3.4001570E-02 0.7242928 at 110iterations 1.9730628E-02 0.4274559 at 120iterations 1.1411952E-02 0.2496414 at 130iterations 6.6335490E-03 0.1503725 at 140iterations 3.8451543E-03 7.7344656E-02 at 150iterations 2.2265520E-03 5.1212311E-02 at 160iterations 1.2912940E-03 2.8246880E-02 at 170iterations 7.5105473E-04 1.5478134E-02 at 180iterations finished qdiffx linear iterations at : 03:25:28 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 7.5105473E-04 1.5478134E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 03:25:29 12.063u 0.188s 0:12.54 97.6% 0+0k 0+0io 0pf+0w