Mon Oct 10 13:55:45 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 Mon Oct 10 2011 at 13:55:45 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1979 !!! WARNING: HIR 237 has a net charge of 0.5140 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: 0.6743702 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): 43.99700 96.78699 ymin,ymax (A): -34.30300 7.134000 zmin,zma (A): 81.85600 128.4930 x,y,z range (A): 52.78999 41.43700 46.63699 scale (grids/A): 0.6743702 object centre (A): 70.39200 -13.58450 105.1745 number of atom coordinates read : 1979 total number of charged atoms : 1748 net assigned charge : 4.514005 assigned positive charge : 281.7570 centred at (gu) : 86.94135 89.40104 90.39486 assigned negative charge : -277.2432 centred at (gu) : 86.93356 89.51125 90.31204 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6056 nv = 96 ne = 84 npr = 40779 no. pairs analyzed = 40779 no. exposed pairs = 2558 no. arc points = 17672 no. surface atoms = 863 nbur = 1116 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3263 m= 1 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1482 ## 110 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6527 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8514679E-10 3.5676052E-08 midg,1,midg; midg,igrid,midg 4.3290918E-08 -5.0906950E-09 1,midg,midg; igrid,midg,midg 2.7367971E-08 9.9656692E-09 gauss-seidel spectral radius is 0.9885428 estimated iterations to convergence 76 setup time was (sec) 0.4900000 now iterating at: 13:55:46 rms-change max change #iterations 0.1572204 28.46530 at 10iterations 1.7719904E-02 2.558781 at 20iterations 2.2170679E-03 0.3968887 at 30iterations 5.0252007E-04 8.1170082E-02 at 40iterations 1.9923851E-04 3.3527374E-02 at 50iterations finished qdiffx linear iterations at : 13:55:48 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.9923851E-04 3.3527374E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:55:49 3.311u 0.222s 0:03.90 90.5% 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 Mon Oct 10 2011 at 13:55:49 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1979 !!! WARNING: HIR 237 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.023111 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): 43.99700 96.78699 ymin,ymax (A): -34.30300 7.134000 zmin,zma (A): 81.85600 128.4930 x,y,z range (A): 52.78999 41.43700 46.63699 scale (grids/A): 2.023111 object centre (A): 70.39200 -13.58450 105.1745 number of atom coordinates read : 1979 total number of charged atoms : 1748 net assigned charge : 4.514005 assigned positive charge : 281.7570 centred at (gu) : 80.82397 88.20313 91.18480 assigned negative charge : -277.2432 centred at (gu) : 80.80071 88.53405 90.93638 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17672 grid for indexing accessible points = 1.400000 m= 25154 mr = 43779 m= 4811 mr = 18376 m= 369 mr = 3053 m= 4 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 28956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 13851 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) : 0.6743702 object centre at (A) : 70.39200 -13.58450 105.1745 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5060286E-03 3.5263643E-02 midg,1,midg; midg,igrid,midg 2.7905956E-02 -9.9132257E-04 1,midg,midg; igrid,midg,midg 4.2933752E-03 -9.1877757E-03 gauss-seidel spectral radius is 0.9987191 estimated iterations to convergence 221 setup time was (sec) 0.8400000 now iterating at: 13:55:50 rms-change max change #iterations 4.044905 212.1072 at 10iterations 1.940769 75.52309 at 20iterations 0.9292236 30.53207 at 30iterations 0.4468175 17.08449 at 40iterations 0.2147734 7.285929 at 50iterations 0.1032071 3.501404 at 60iterations 4.9336258E-02 1.724549 at 70iterations 2.3877526E-02 0.8474731 at 80iterations 1.1514436E-02 0.3937206 at 90iterations 5.6458530E-03 0.1922379 at 100iterations 2.8108729E-03 9.6557617E-02 at 110iterations 1.4708193E-03 5.3032875E-02 at 120iterations finished qdiffx linear iterations at : 13:55:57 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 1.4708193E-03 5.3032875E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 13:55:57 7.458u 0.212s 0:08.15 93.9% 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 Mon Oct 10 2011 at 13:55:57 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1979 !!! WARNING: HIR 237 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.034666 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): 43.99700 96.78699 ymin,ymax (A): -34.30300 7.134000 zmin,zma (A): 81.85600 128.4930 x,y,z range (A): 52.78999 41.43700 46.63699 scale (grids/A): 3.034666 object centre (A): 70.39200 -13.58450 105.1745 number of atom coordinates read : 1979 total number of charged atoms : 1748 net assigned charge : 4.514005 assigned positive charge : 281.7570 centred at (gu) : 76.23605 87.30467 91.77739 assigned negative charge : -277.2432 centred at (gu) : 76.20109 87.80107 91.40463 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 147279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17672 grid for indexing accessible points = 1.400000 m= 77812 mr = 105829 m= 31660 mr = 63266 m= 8926 mr = 25328 m= 1591 mr = 6668 m= 166 mr = 1095 m= 7 mr = 97 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 65157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 13984 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) : 2.023111 object centre at (A) : 70.39200 -13.58450 105.1745 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2330297E-02 0.3562296 midg,1,midg; midg,igrid,midg 0.2582608 -1.0977912E-02 1,midg,midg; igrid,midg,midg -5.3998549E-02 -7.9619311E-02 gauss-seidel spectral radius is 0.9992739 estimated iterations to convergence 293 setup time was (sec) 1.540000 now iterating at: 13:55:59 rms-change max change #iterations 9.299778 321.8768 at 10iterations 5.498605 156.4669 at 20iterations 3.249068 90.05004 at 30iterations 1.906453 46.38581 at 40iterations 1.112613 23.02188 at 50iterations 0.6503460 13.19884 at 60iterations 0.3795021 8.111681 at 70iterations 0.2205161 4.364092 at 80iterations 0.1281284 2.617829 at 90iterations 7.4498691E-02 1.446607 at 100iterations 4.3184776E-02 0.8907375 at 110iterations 2.5099277E-02 0.4627371 at 120iterations 1.4590964E-02 0.3187103 at 130iterations 8.5304240E-03 0.1916313 at 140iterations 5.0236187E-03 9.9504471E-02 at 150iterations 3.0023754E-03 6.0770035E-02 at 160iterations 1.8461035E-03 3.6487579E-02 at 170iterations 1.2000825E-03 2.3813725E-02 at 180iterations finished qdiffx linear iterations at : 13:56:10 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 1.2000825E-03 2.3813725E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 13:56:10 12.419u 0.245s 0:13.14 96.2% 0+0k 0+0io 0pf+0w