Mon Oct 10 13:58:53 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 13:58:53 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 = 4235 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: 0.5916079 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): -24.96400 35.21100 ymin,ymax (A): 34.83800 92.33500 zmin,zma (A): 30.82600 89.67800 x,y,z range (A): 60.17500 57.49700 58.85200 scale (grids/A): 0.5916079 object centre (A): 5.123500 63.58650 60.25200 number of atom coordinates read : 4235 total number of charged atoms : 4099 net assigned charge : 4.1961670E-05 assigned positive charge : 637.2844 centred at (gu) : 90.88182 89.55987 88.66038 assigned negative charge : -637.2875 centred at (gu) : 90.70176 89.67764 88.85459 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9479 nv = 96 ne = 84 npr = 89296 no. pairs analyzed = 89296 no. exposed pairs = 4768 no. arc points = 32149 no. surface atoms = 1619 nbur = 2616 mkacc time = 0.2400000 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= 467 mr = 5587 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 0.5100000 number of dielectric boundary points 4303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3430 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 12468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1663970E-08 -6.8496289E-09 midg,1,midg; midg,igrid,midg 5.6727791E-09 -5.1515214E-09 1,midg,midg; igrid,midg,midg -7.0617969E-09 9.6976809E-09 gauss-seidel spectral radius is 0.9853376 estimated iterations to convergence 68 setup time was (sec) 0.9900000 now iterating at: 13:58:55 rms-change max change #iterations 0.1328466 17.31779 at 10iterations 1.1512955E-02 1.435819 at 20iterations 1.2718721E-03 0.1623840 at 30iterations 2.7272481E-04 3.2184601E-02 at 40iterations 8.7205219E-05 1.0576129E-02 at 50iterations finished qdiffx linear iterations at : 13:59:02 total time elapsed so far: 7.990000 # loops : 50 mean,max change (kT/e) : 8.7205219E-05 1.0576129E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 13:59:03 8.178u 0.727s 0:09.56 92.9% 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 13:59:03 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 = 4235 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: 1.774824 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): -24.96400 35.21100 ymin,ymax (A): 34.83800 92.33500 zmin,zma (A): 30.82600 89.67800 x,y,z range (A): 60.17500 57.49700 58.85200 scale (grids/A): 1.774824 object centre (A): 5.123500 63.58650 60.25200 number of atom coordinates read : 4235 total number of charged atoms : 4099 net assigned charge : 4.1961670E-05 assigned positive charge : 637.2844 centred at (gu) : 92.64408 88.67825 85.97986 assigned negative charge : -637.2875 centred at (gu) : 92.10479 89.03251 86.56322 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 105442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32149 grid for indexing accessible points = 1.400000 m= 36571 mr = 76978 m= 4958 mr = 27235 m= 236 mr = 3175 m= 0 mr = 83 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 7019 time to turn everything in is 0.9900000 number of dielectric boundary points 39736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 31935 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) : 0.5916079 object centre at (A) : 5.123500 63.58650 60.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9760991E-02 -3.9734352E-02 midg,1,midg; midg,igrid,midg 2.8326450E-02 -2.6368957E-02 1,midg,midg; igrid,midg,midg -1.0974252E-02 5.2947737E-02 gauss-seidel spectral radius is 0.9985749 estimated iterations to convergence 210 setup time was (sec) 1.570000 now iterating at: 13:59:05 rms-change max change #iterations 4.905277 236.2214 at 10iterations 2.253808 62.50561 at 20iterations 1.039755 29.16210 at 30iterations 0.4792260 13.48631 at 40iterations 0.2218325 5.954235 at 50iterations 0.1024466 2.904707 at 60iterations 4.7375631E-02 1.280679 at 70iterations 2.1838944E-02 0.5790417 at 80iterations 1.0139292E-02 0.2778554 at 90iterations 4.7046002E-03 0.1268368 at 100iterations 2.2002317E-03 6.1983109E-02 at 110iterations 1.0444265E-03 2.9502869E-02 at 120iterations finished qdiffx linear iterations at : 13:59:22 total time elapsed so far: 18.27000 # loops : 120 mean,max change (kT/e) : 1.0444265E-03 2.9502869E-02 energy calculations done at 18.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.46000 DelPhi exited at 13:59:24 18.463u 0.841s 0:21.10 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 13:59:24 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 = 4235 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: 2.662235 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): -24.96400 35.21100 ymin,ymax (A): 34.83800 92.33500 zmin,zma (A): 30.82600 89.67800 x,y,z range (A): 60.17500 57.49700 58.85200 scale (grids/A): 2.662235 object centre (A): 5.123500 63.58650 60.25200 number of atom coordinates read : 4235 total number of charged atoms : 4099 net assigned charge : 4.1961670E-05 assigned positive charge : 637.2844 centred at (gu) : 93.96604 88.01685 83.96950 assigned negative charge : -637.2875 centred at (gu) : 93.15714 88.54865 84.84473 start vw surface at 0.1600000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 245032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32149 grid for indexing accessible points = 1.400000 m= 122566 mr = 186422 m= 40190 mr = 101685 m= 8767 mr = 32415 m= 1082 mr = 6832 m= 25 mr = 708 m= 0 mr = 0 time to grow re-entrant surface = 1.530000 no. cavity mid-points inaccessible to solvent = 23383 time to turn everything in is 2.440000 number of dielectric boundary points 89600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.770000 number of grid points assigned charge 32783 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) : 1.774824 object centre at (A) : 5.123500 63.58650 60.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8734981 -0.4858647 midg,1,midg; midg,igrid,midg 0.3258475 -0.2471238 1,midg,midg; igrid,midg,midg 9.5655642E-02 0.4421467 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 3.140000 now iterating at: 13:59:28 rms-change max change #iterations 11.79969 303.0093 at 10iterations 6.966215 164.0585 at 20iterations 4.071774 76.16225 at 30iterations 2.377440 64.00437 at 40iterations 1.386851 24.53420 at 50iterations 0.8043825 14.22991 at 60iterations 0.4659781 7.602965 at 70iterations 0.2701173 4.264093 at 80iterations 0.1562797 2.850245 at 90iterations 9.0415731E-02 1.405839 at 100iterations 5.2241806E-02 0.8835943 at 110iterations 3.0197939E-02 0.4863958 at 120iterations 1.7490508E-02 0.2633591 at 130iterations 1.0112291E-02 0.1706448 at 140iterations 5.8979588E-03 8.7562561E-02 at 150iterations 3.4472446E-03 5.4072857E-02 at 160iterations 2.0393727E-03 3.1530380E-02 at 170iterations 1.2294532E-03 1.9923210E-02 at 180iterations finished qdiffx linear iterations at : 13:59:55 total time elapsed so far: 30.71000 # loops : 180 mean,max change (kT/e) : 1.2294532E-03 1.9923210E-02 energy calculations done at 30.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.90000 DelPhi exited at 13:59:56 30.900u 0.770s 0:32.71 96.8% 0+0k 0+0io 0pf+0w