Mon Oct 10 14:25:13 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 14:25:13 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 0.6063393 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): -23.68700 22.52400 ymin,ymax (A): -23.99000 34.72300 zmin,zma (A): -37.12700 15.63600 x,y,z range (A): 46.21100 58.71300 52.76300 scale (grids/A): 0.6063393 object centre (A): -0.5815001 5.366500 -10.74550 number of atom coordinates read : 2298 total number of charged atoms : 2144 net assigned charge : 2.000002 assigned positive charge : 333.2764 centred at (gu) : 89.18294 89.82111 89.93501 assigned negative charge : -331.2768 centred at (gu) : 89.11149 89.66048 89.88135 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5750 nv = 96 ne = 84 npr = 45711 no. pairs analyzed = 45711 no. exposed pairs = 3200 no. arc points = 22230 no. surface atoms = 1070 nbur = 1228 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 2829 m= 0 mr = 16 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2238 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6986 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6040209E-10 3.0679521E-09 midg,1,midg; midg,igrid,midg -5.3074753E-09 6.7796244E-09 1,midg,midg; igrid,midg,midg -1.9776620E-09 3.1430980E-09 gauss-seidel spectral radius is 0.9859030 estimated iterations to convergence 69 setup time was (sec) 0.6400000 now iterating at: 14:25:14 rms-change max change #iterations 0.1011891 15.92844 at 10iterations 8.6719692E-03 1.434112 at 20iterations 7.5454888E-04 0.1240911 at 30iterations 6.5092565E-05 1.1360168E-02 at 40iterations 5.8383403E-06 1.0547638E-03 at 50iterations finished qdiffx linear iterations at : 14:25:17 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 5.8383403E-06 1.0547638E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 14:25:18 4.191u 0.222s 0:04.79 92.0% 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 14:25:18 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 1.819018 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): -23.68700 22.52400 ymin,ymax (A): -23.99000 34.72300 zmin,zma (A): -37.12700 15.63600 x,y,z range (A): 46.21100 58.71300 52.76300 scale (grids/A): 1.819018 object centre (A): -0.5815001 5.366500 -10.74550 number of atom coordinates read : 2298 total number of charged atoms : 2144 net assigned charge : 2.000002 assigned positive charge : 333.2764 centred at (gu) : 87.54856 89.46300 89.80470 assigned negative charge : -331.2768 centred at (gu) : 87.33435 88.98139 89.64390 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 62162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22230 grid for indexing accessible points = 1.400000 m= 20783 mr = 40738 m= 2722 mr = 14324 m= 117 mr = 1336 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 29371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 16758 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) : 0.6063393 object centre at (A) : -0.5815001 5.366500 -10.74550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5331841E-03 6.8704323E-03 midg,1,midg; midg,igrid,midg 2.5401518E-03 4.4739014E-03 1,midg,midg; igrid,midg,midg 1.1346679E-03 5.1260879E-03 gauss-seidel spectral radius is 0.9984866 estimated iterations to convergence 204 setup time was (sec) 0.9800000 now iterating at: 14:25:19 rms-change max change #iterations 3.529811 198.3089 at 10iterations 1.572959 59.60583 at 20iterations 0.7065581 25.63057 at 30iterations 0.3166198 12.74741 at 40iterations 0.1417581 4.858013 at 50iterations 6.3912868E-02 2.518784 at 60iterations 2.8667416E-02 1.160627 at 70iterations 1.2862096E-02 0.4579029 at 80iterations 5.7759667E-03 0.2115852 at 90iterations 2.5990168E-03 9.6236229E-02 at 100iterations 1.1660128E-03 4.3235779E-02 at 110iterations 5.2489829E-04 1.8869400E-02 at 120iterations finished qdiffx linear iterations at : 14:25:27 total time elapsed so far: 9.040000 # loops : 120 mean,max change (kT/e) : 5.2489829E-04 1.8869400E-02 energy calculations done at 9.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 14:25:28 9.281u 0.220s 0:09.82 96.7% 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 14:25:28 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 2.728527 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): -23.68700 22.52400 ymin,ymax (A): -23.99000 34.72300 zmin,zma (A): -37.12700 15.63600 x,y,z range (A): 46.21100 58.71300 52.76300 scale (grids/A): 2.728527 object centre (A): -0.5815001 5.366500 -10.74550 number of atom coordinates read : 2298 total number of charged atoms : 2144 net assigned charge : 2.000002 assigned positive charge : 333.2764 centred at (gu) : 86.32260 89.19447 89.70708 assigned negative charge : -331.2768 centred at (gu) : 86.00150 88.47206 89.46581 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 143861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22230 grid for indexing accessible points = 1.400000 m= 68878 mr = 99866 m= 22513 mr = 54157 m= 4454 mr = 16964 m= 444 mr = 2810 m= 20 mr = 204 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 66166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 17150 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) : 1.819018 object centre at (A) : -0.5815001 5.366500 -10.74550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1557145 8.1222393E-02 midg,1,midg; midg,igrid,midg 0.1384708 -9.1949202E-02 1,midg,midg; igrid,midg,midg 3.9991099E-02 3.3961710E-02 gauss-seidel spectral radius is 0.9992217 estimated iterations to convergence 283 setup time was (sec) 1.850000 now iterating at: 14:25:30 rms-change max change #iterations 8.690752 295.8282 at 10iterations 5.070136 134.1467 at 20iterations 2.935494 74.92828 at 30iterations 1.691241 39.33172 at 40iterations 0.9695123 24.39158 at 50iterations 0.5538141 13.48415 at 60iterations 0.3164860 10.10019 at 70iterations 0.1796607 3.677860 at 80iterations 0.1022696 2.118898 at 90iterations 5.8179960E-02 1.321558 at 100iterations 3.3103354E-02 0.6673946 at 110iterations 1.8725608E-02 0.3932462 at 120iterations 1.0633540E-02 0.2459106 at 130iterations 6.0235057E-03 0.1249027 at 140iterations 3.4148050E-03 6.9939613E-02 at 150iterations 1.9349013E-03 3.8151503E-02 at 160iterations 1.0945675E-03 2.4120331E-02 at 170iterations 6.1969215E-04 1.3526917E-02 at 180iterations finished qdiffx linear iterations at : 14:25:43 total time elapsed so far: 14.72000 # loops : 180 mean,max change (kT/e) : 6.1969215E-04 1.3526917E-02 energy calculations done at 14.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.96000 DelPhi exited at 14:25:43 14.961u 0.248s 0:15.59 97.4% 0+0k 0+0io 0pf+0w