Mon Oct 10 21:19:38 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 21:19:38 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2813 !!! WARNING: HIR 107 has a net charge of 0.5140 !!! WARNING: HIR 233 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6062670 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): -9.400000 42.72700 ymin,ymax (A): -0.8320000 57.50900 zmin,zma (A): -21.39300 37.32700 x,y,z range (A): 52.12700 58.34100 58.72000 scale (grids/A): 0.6062670 object centre (A): 16.66350 28.33850 7.967000 number of atom coordinates read : 2813 total number of charged atoms : 2673 net assigned charge : 1.528010 assigned positive charge : 423.4275 centred at (gu) : 89.79086 89.26793 88.81391 assigned negative charge : -421.9008 centred at (gu) : 89.71700 89.31589 88.73644 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7051 nv = 96 ne = 84 npr = 55192 no. pairs analyzed = 55192 no. exposed pairs = 3869 no. arc points = 28173 no. surface atoms = 1283 nbur = 1530 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3413 m= 3 mr = 31 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 0.3700000 number of dielectric boundary points 3923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2847 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8402219E-09 3.4644780E-09 midg,1,midg; midg,igrid,midg 3.6963315E-09 -1.2398003E-09 1,midg,midg; igrid,midg,midg -2.8685168E-09 4.1538741E-09 gauss-seidel spectral radius is 0.9859502 estimated iterations to convergence 69 setup time was (sec) 0.6000000 now iterating at: 21:19:39 rms-change max change #iterations 0.1182273 17.67281 at 10iterations 1.0183633E-02 1.563643 at 20iterations 9.2856213E-04 0.1349545 at 30iterations 9.8880708E-05 1.3898849E-02 at 40iterations 1.5361320E-05 2.4986267E-03 at 50iterations finished qdiffx linear iterations at : 21:19:42 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.5361320E-05 2.4986267E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 21:19:42 3.397u 0.152s 0:03.97 89.1% 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 21:19:42 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2813 !!! WARNING: HIR 107 has a net charge of 0.5140 !!! WARNING: HIR 233 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.818801 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): -9.400000 42.72700 ymin,ymax (A): -0.8320000 57.50900 zmin,zma (A): -21.39300 37.32700 x,y,z range (A): 52.12700 58.34100 58.72000 scale (grids/A): 1.818801 object centre (A): 16.66350 28.33850 7.967000 number of atom coordinates read : 2813 total number of charged atoms : 2673 net assigned charge : 1.528010 assigned positive charge : 423.4275 centred at (gu) : 89.37167 87.80312 86.44101 assigned negative charge : -421.9008 centred at (gu) : 89.15097 87.94734 86.20927 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28173 grid for indexing accessible points = 1.400000 m= 25107 mr = 49779 m= 3645 mr = 17295 m= 197 mr = 1952 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 478 time to turn everything in is 0.6100000 number of dielectric boundary points 36200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20902 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) : 0.6062670 object centre at (A) : 16.66350 28.33850 7.967000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6894634E-02 -4.1457801E-03 midg,1,midg; midg,igrid,midg -1.2582177E-04 -1.8810641E-02 1,midg,midg; igrid,midg,midg 9.2155123E-03 2.2141725E-02 gauss-seidel spectral radius is 0.9985535 estimated iterations to convergence 208 setup time was (sec) 0.8900000 now iterating at: 21:19:43 rms-change max change #iterations 4.089611 189.7242 at 10iterations 1.852156 62.10112 at 20iterations 0.8479003 31.52612 at 30iterations 0.3875074 12.48713 at 40iterations 0.1768199 6.030416 at 50iterations 8.0804206E-02 3.048767 at 60iterations 3.6987189E-02 1.311394 at 70iterations 1.6861616E-02 0.5387983 at 80iterations 7.7463812E-03 0.2375145 at 90iterations 3.5394323E-03 0.1117642 at 100iterations 1.6213376E-03 5.1463962E-02 at 110iterations 7.4515719E-04 2.5088310E-02 at 120iterations finished qdiffx linear iterations at : 21:19:50 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 7.4515719E-04 2.5088310E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 21:19:50 7.499u 0.175s 0:07.99 95.8% 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 21:19:51 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2813 !!! WARNING: HIR 107 has a net charge of 0.5140 !!! WARNING: HIR 233 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.728202 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): -9.400000 42.72700 ymin,ymax (A): -0.8320000 57.50900 zmin,zma (A): -21.39300 37.32700 x,y,z range (A): 52.12700 58.34100 58.72000 scale (grids/A): 2.728202 object centre (A): 16.66350 28.33850 7.967000 number of atom coordinates read : 2813 total number of charged atoms : 2673 net assigned charge : 1.528010 assigned positive charge : 423.4275 centred at (gu) : 89.05735 86.70448 84.66138 assigned negative charge : -421.9008 centred at (gu) : 88.72642 86.92098 84.31388 start vw surface at 0.2400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 176472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28173 grid for indexing accessible points = 1.400000 m= 81603 mr = 121594 m= 28148 mr = 63646 m= 6160 mr = 21649 m= 768 mr = 4301 m= 34 mr = 435 m= 0 mr = 10 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 1601 time to turn everything in is 1.470000 number of dielectric boundary points 81550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 21377 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) : 1.818801 object centre at (A) : 16.66350 28.33850 7.967000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5865460 -7.8003705E-02 midg,1,midg; midg,igrid,midg -7.9768814E-02 -0.2803965 1,midg,midg; igrid,midg,midg 0.1095602 0.2496167 gauss-seidel spectral radius is 0.9992536 estimated iterations to convergence 289 setup time was (sec) 1.780000 now iterating at: 21:19:52 rms-change max change #iterations 9.910120 306.4637 at 10iterations 5.846727 152.0441 at 20iterations 3.405284 74.01891 at 30iterations 1.981805 40.59801 at 40iterations 1.145703 26.87520 at 50iterations 0.6612941 12.06939 at 60iterations 0.3814881 7.521553 at 70iterations 0.2196371 4.118599 at 80iterations 0.1264195 2.989416 at 90iterations 7.2777934E-02 1.357644 at 100iterations 4.1804500E-02 0.7195311 at 110iterations 2.3913607E-02 0.4971428 at 120iterations 1.3726587E-02 0.2436213 at 130iterations 7.8969738E-03 0.1434371 at 140iterations 4.5229909E-03 8.8502884E-02 at 150iterations 2.5928949E-03 4.7863007E-02 at 160iterations 1.4910839E-03 2.7885437E-02 at 170iterations 8.5545238E-04 1.5548706E-02 at 180iterations finished qdiffx linear iterations at : 21:20:03 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 8.5545238E-04 1.5548706E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 21:20:03 12.400u 0.177s 0:12.87 97.6% 0+0k 0+0io 0pf+0w