Mon Oct 10 14:37:31 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 14:37:31 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5918832 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 0.5918832 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 423.3494 centred at (gu) : 91.98691 89.62823 89.41725 assigned negative charge : -426.9503 centred at (gu) : 91.92326 89.71574 89.49067 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6348 nv = 96 ne = 84 npr = 54066 no. pairs analyzed = 54066 no. exposed pairs = 3672 no. arc points = 25444 no. surface atoms = 1232 nbur = 1499 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 331 mr = 3269 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2581 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1706522E-09 -3.0927956E-09 midg,1,midg; midg,igrid,midg 1.5782879E-09 -3.6538519E-09 1,midg,midg; igrid,midg,midg -2.0553477E-09 1.1891479E-09 gauss-seidel spectral radius is 0.9852448 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 14:37:32 rms-change max change #iterations 0.1075800 16.26665 at 10iterations 8.9303385E-03 1.324512 at 20iterations 7.4250088E-04 0.1347466 at 30iterations 7.9812373E-05 1.1840820E-02 at 40iterations 1.4255810E-05 2.2659302E-03 at 50iterations finished qdiffx linear iterations at : 14:37:35 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 1.4255810E-05 2.2659302E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 14:37:35 3.653u 0.224s 0:04.23 91.4% 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 14:37:35 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.775650 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 1.775650 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 423.3494 centred at (gu) : 95.96011 88.88414 88.25081 assigned negative charge : -426.9503 centred at (gu) : 95.76930 89.14703 88.47173 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69131 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25444 grid for indexing accessible points = 1.400000 m= 23215 mr = 46424 m= 3164 mr = 16150 m= 156 mr = 1695 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 31371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20183 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) : 0.5918832 object centre at (A) : 22.11550 9.139500 103.6845 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8280199E-03 -2.9905392E-02 midg,1,midg; midg,igrid,midg -7.1762232E-03 -1.7686596E-02 1,midg,midg; igrid,midg,midg 1.8790323E-02 3.1390786E-02 gauss-seidel spectral radius is 0.9984558 estimated iterations to convergence 202 setup time was (sec) 0.6100000 now iterating at: 14:37:36 rms-change max change #iterations 3.939189 192.0708 at 10iterations 1.751561 60.06523 at 20iterations 0.7774522 27.56125 at 30iterations 0.3474615 12.28454 at 40iterations 0.1546435 5.900093 at 50iterations 6.9200635E-02 2.530849 at 60iterations 3.0797815E-02 0.9878343 at 70iterations 1.3713860E-02 0.4822884 at 80iterations 6.1293351E-03 0.2041683 at 90iterations 2.7592068E-03 9.1815948E-02 at 100iterations 1.2352122E-03 4.3278873E-02 at 110iterations 5.5910641E-04 1.8617630E-02 at 120iterations finished qdiffx linear iterations at : 14:37:44 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 5.5910641E-04 1.8617630E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 14:37:44 8.256u 0.242s 0:08.80 96.4% 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 14:37:44 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.663474 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): -7.958000 52.18900 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.42900 129.9400 x,y,z range (A): 60.14700 50.63700 52.51100 scale (grids/A): 2.663474 object centre (A): 22.11550 9.139500 103.6845 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -3.599991 assigned positive charge : 423.3494 centred at (gu) : 98.94003 88.32603 87.37611 assigned negative charge : -426.9503 centred at (gu) : 98.65377 88.72051 87.70747 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 160122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25444 grid for indexing accessible points = 1.400000 m= 76958 mr = 113526 m= 25377 mr = 60544 m= 5330 mr = 19447 m= 607 mr = 3691 m= 14 mr = 331 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 70869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 20706 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) : 1.775650 object centre at (A) : 22.11550 9.139500 103.6845 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1067559 -0.3841687 midg,1,midg; midg,igrid,midg -0.1124156 -0.1805314 1,midg,midg; igrid,midg,midg 0.3748127 0.3032138 gauss-seidel spectral radius is 0.9992165 estimated iterations to convergence 282 setup time was (sec) 1.160000 now iterating at: 14:37:46 rms-change max change #iterations 9.721912 314.9765 at 10iterations 5.632352 131.5104 at 20iterations 3.233712 67.74866 at 30iterations 1.850363 39.68278 at 40iterations 1.054625 23.32207 at 50iterations 0.6000052 12.88362 at 60iterations 0.3410191 7.271612 at 70iterations 0.1937019 4.068077 at 80iterations 0.1097120 2.246229 at 90iterations 6.2008135E-02 1.277050 at 100iterations 3.5179980E-02 0.7049942 at 110iterations 1.9888567E-02 0.3873873 at 120iterations 1.1248034E-02 0.2166147 at 130iterations 6.3628126E-03 0.1356068 at 140iterations 3.6028596E-03 6.8893433E-02 at 150iterations 2.0373906E-03 3.8932800E-02 at 160iterations 1.1539623E-03 2.3450851E-02 at 170iterations 6.5419136E-04 1.2135744E-02 at 180iterations finished qdiffx linear iterations at : 14:37:57 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 6.5419136E-04 1.2135744E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 14:37:58 12.696u 0.289s 0:13.56 95.6% 0+0k 0+0io 0pf+0w