Sun Oct 9 04:46:55 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 Sun Oct 9 2011 at 04:46:55 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 = 2716 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: 0.6149382 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): -10.63100 35.20500 ymin,ymax (A): 4.6000004E-02 57.93800 zmin,zma (A): -25.19700 27.23700 x,y,z range (A): 45.83600 57.89200 52.43400 scale (grids/A): 0.6149382 object centre (A): 12.28700 28.99200 1.020000 number of atom coordinates read : 2716 total number of charged atoms : 2578 net assigned charge : 6.500036 assigned positive charge : 402.1072 centred at (gu) : 90.11811 88.78766 89.65261 assigned negative charge : -395.6085 centred at (gu) : 90.21432 88.67485 89.63387 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6895 nv = 96 ne = 84 npr = 53910 no. pairs analyzed = 53910 no. exposed pairs = 3732 no. arc points = 25862 no. surface atoms = 1255 nbur = 1461 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3452 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2580 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8469 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7497183E-09 5.2593983E-09 midg,1,midg; midg,igrid,midg -2.8368632E-09 8.4861638E-09 1,midg,midg; igrid,midg,midg 9.8707362E-09 -1.1310365E-09 gauss-seidel spectral radius is 0.9863241 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 04:46:56 rms-change max change #iterations 0.1198126 18.78294 at 10iterations 1.0787374E-02 1.628554 at 20iterations 9.5617038E-04 0.1364288 at 30iterations 1.0454398E-04 1.8516541E-02 at 40iterations 2.3366845E-05 3.9415359E-03 at 50iterations finished qdiffx linear iterations at : 04:47:00 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 2.3366845E-05 3.9415359E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 04:47:00 4.082u 0.264s 0:04.71 92.1% 0+0k 0+0io 6pf+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 Sun Oct 9 2011 at 04:47:00 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 = 2716 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: 1.844815 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): -10.63100 35.20500 ymin,ymax (A): 4.6000004E-02 57.93800 zmin,zma (A): -25.19700 27.23700 x,y,z range (A): 45.83600 57.89200 52.43400 scale (grids/A): 1.844815 object centre (A): 12.28700 28.99200 1.020000 number of atom coordinates read : 2716 total number of charged atoms : 2578 net assigned charge : 6.500036 assigned positive charge : 402.1072 centred at (gu) : 90.35342 86.36246 88.95711 assigned negative charge : -395.6085 centred at (gu) : 90.64277 86.02423 88.90128 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25862 grid for indexing accessible points = 1.400000 m= 24739 mr = 49570 m= 3605 mr = 16971 m= 193 mr = 1912 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 34603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20200 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) : 0.6149382 object centre at (A) : 12.28700 28.99200 1.020000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1670873E-03 -6.6399463E-03 midg,1,midg; midg,igrid,midg 5.7798261E-03 1.7644141E-02 1,midg,midg; igrid,midg,midg 2.2339549E-02 3.6606393E-03 gauss-seidel spectral radius is 0.9985703 estimated iterations to convergence 210 setup time was (sec) 0.9700000 now iterating at: 04:47:01 rms-change max change #iterations 4.031159 182.8641 at 10iterations 1.850906 73.74100 at 20iterations 0.8518031 27.85485 at 30iterations 0.3911553 13.37426 at 40iterations 0.1800246 6.249441 at 50iterations 8.2790665E-02 2.720952 at 60iterations 3.8165413E-02 1.192524 at 70iterations 1.7483922E-02 0.6938248 at 80iterations 8.0860807E-03 0.2583065 at 90iterations 3.7155629E-03 0.1325046 at 100iterations 1.7213913E-03 5.4356690E-02 at 110iterations 8.0524111E-04 2.4723053E-02 at 120iterations finished qdiffx linear iterations at : 04:47:10 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 8.0524111E-04 2.4723053E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 04:47:10 9.484u 0.293s 0:10.08 96.9% 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 Sun Oct 9 2011 at 04:47:10 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 = 2716 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: 2.767222 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): -10.63100 35.20500 ymin,ymax (A): 4.6000004E-02 57.93800 zmin,zma (A): -25.19700 27.23700 x,y,z range (A): 45.83600 57.89200 52.43400 scale (grids/A): 2.767222 object centre (A): 12.28700 28.99200 1.020000 number of atom coordinates read : 2716 total number of charged atoms : 2578 net assigned charge : 6.500036 assigned positive charge : 402.1072 centred at (gu) : 90.53007 84.54339 88.43533 assigned negative charge : -395.6085 centred at (gu) : 90.96407 84.03629 88.35180 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 172714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25862 grid for indexing accessible points = 1.400000 m= 82239 mr = 121453 m= 27152 mr = 64449 m= 6113 mr = 20439 m= 815 mr = 4155 m= 42 mr = 468 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 78100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 20622 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) : 1.844815 object centre at (A) : 12.28700 28.99200 1.020000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1844872 -4.4910284E-03 midg,1,midg; midg,igrid,midg 9.1315655E-04 0.2045096 1,midg,midg; igrid,midg,midg 0.2181781 6.2047273E-02 gauss-seidel spectral radius is 0.9992533 estimated iterations to convergence 289 setup time was (sec) 2.030000 now iterating at: 04:47:13 rms-change max change #iterations 9.787765 350.7041 at 10iterations 5.773757 148.0394 at 20iterations 3.373586 72.17017 at 30iterations 1.954993 43.39798 at 40iterations 1.133230 24.18958 at 50iterations 0.6547091 12.20661 at 60iterations 0.3779084 8.040783 at 70iterations 0.2178491 4.392090 at 80iterations 0.1253690 2.654454 at 90iterations 7.2154254E-02 1.390258 at 100iterations 4.1383892E-02 0.8321912 at 110iterations 2.3762843E-02 0.4521407 at 120iterations 1.3640204E-02 0.2517185 at 130iterations 7.8406800E-03 0.1411781 at 140iterations 4.5013796E-03 8.0970764E-02 at 150iterations 2.5881561E-03 4.7865629E-02 at 160iterations 1.4884042E-03 2.8404236E-02 at 170iterations 8.6335250E-04 1.9580841E-02 at 180iterations finished qdiffx linear iterations at : 04:47:26 total time elapsed so far: 15.77000 # loops : 180 mean,max change (kT/e) : 8.6335250E-04 1.9580841E-02 energy calculations done at 15.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 04:47:27 15.943u 0.297s 0:16.51 98.3% 0+0k 0+0io 0pf+0w