Mon Oct 10 17:10:21 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 17:10:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1838 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: 0.6999469 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): -27.22700 23.63400 ymin,ymax (A): -2.674000 38.09800 zmin,zma (A): 26.24700 76.41900 x,y,z range (A): 50.86100 40.77200 50.17200 scale (grids/A): 0.6999469 object centre (A): -1.796500 17.71200 51.33300 number of atom coordinates read : 1838 total number of charged atoms : 1708 net assigned charge : -6.999989 assigned positive charge : 258.6214 centred at (gu) : 88.44667 90.08525 91.11063 assigned negative charge : -265.6212 centred at (gu) : 88.50063 90.21487 91.23936 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6177 nv = 96 ne = 84 npr = 38444 no. pairs analyzed = 38444 no. exposed pairs = 2360 no. arc points = 17331 no. surface atoms = 793 nbur = 1045 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3240 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 94 time to turn everything in is 0.2300000 number of dielectric boundary points 3226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1466 ## 109 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6763 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5858434E-09 -1.1828917E-07 midg,1,midg; midg,igrid,midg -3.5243060E-09 -9.6979242E-08 1,midg,midg; igrid,midg,midg -3.9693695E-08 -5.0578198E-08 gauss-seidel spectral radius is 0.9893513 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 17:10:34 rms-change max change #iterations 0.1792201 32.06134 at 10iterations 2.1100951E-02 3.194370 at 20iterations 2.5083686E-03 0.3541794 at 30iterations 3.0343031E-04 4.6043396E-02 at 40iterations 3.6433652E-05 5.7325363E-03 at 50iterations finished qdiffx linear iterations at : 17:10:38 total time elapsed so far: 4.720000 # loops : 50 mean,max change (kT/e) : 3.6433652E-05 5.7325363E-03 energy calculations done at 4.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.870000 DelPhi exited at 17:10:39 4.876u 0.527s 0:17.68 30.4% 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 17:10:39 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1838 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: 2.099841 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): -27.22700 23.63400 ymin,ymax (A): -2.674000 38.09800 zmin,zma (A): 26.24700 76.41900 x,y,z range (A): 50.86100 40.77200 50.17200 scale (grids/A): 2.099841 object centre (A): -1.796500 17.71200 51.33300 number of atom coordinates read : 1838 total number of charged atoms : 1708 net assigned charge : -6.999989 assigned positive charge : 258.6214 centred at (gu) : 85.34016 90.25612 93.33219 assigned negative charge : -265.6212 centred at (gu) : 85.50214 90.64476 93.71819 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 65893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17331 grid for indexing accessible points = 1.400000 m= 23244 mr = 44110 m= 4007 mr = 16743 m= 305 mr = 2503 m= 9 mr = 139 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2091 time to turn everything in is 0.5400000 number of dielectric boundary points 29959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 13558 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) : 0.6999469 object centre at (A) : -1.796500 17.71200 51.33300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5915230E-02 -8.8924460E-02 midg,1,midg; midg,igrid,midg 9.4208088E-05 -2.2645438E-02 1,midg,midg; igrid,midg,midg 2.1261251E-02 5.5036587E-03 gauss-seidel spectral radius is 0.9988023 estimated iterations to convergence 229 setup time was (sec) 0.8700000 now iterating at: 17:10:40 rms-change max change #iterations 4.115274 183.0505 at 10iterations 2.007053 72.91556 at 20iterations 0.9817724 33.48295 at 30iterations 0.4819784 15.25522 at 40iterations 0.2372076 7.704615 at 50iterations 0.1158826 3.825794 at 60iterations 5.6895196E-02 1.795944 at 70iterations 2.7907489E-02 0.8760834 at 80iterations 1.3682407E-02 0.4479403 at 90iterations 6.7202616E-03 0.2063341 at 100iterations 3.2949941E-03 9.5598221E-02 at 110iterations 1.6164291E-03 4.8927307E-02 at 120iterations finished qdiffx linear iterations at : 17:10:51 total time elapsed so far: 11.60000 # loops : 120 mean,max change (kT/e) : 1.6164291E-03 4.8927307E-02 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 17:10:51 11.768u 0.531s 0:12.63 97.3% 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 17:10:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1838 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: 3.149761 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): -27.22700 23.63400 ymin,ymax (A): -2.674000 38.09800 zmin,zma (A): 26.24700 76.41900 x,y,z range (A): 50.86100 40.77200 50.17200 scale (grids/A): 3.149761 object centre (A): -1.796500 17.71200 51.33300 number of atom coordinates read : 1838 total number of charged atoms : 1708 net assigned charge : -6.999989 assigned positive charge : 258.6214 centred at (gu) : 83.01031 90.38419 94.99832 assigned negative charge : -265.6212 centred at (gu) : 83.25325 90.96723 95.57729 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 151954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17331 grid for indexing accessible points = 1.400000 m= 74121 mr = 106696 m= 27584 mr = 59826 m= 7349 mr = 22001 m= 1280 mr = 5478 m= 127 mr = 906 m= 3 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 7193 time to turn everything in is 1.670000 number of dielectric boundary points 67428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 13664 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) : 2.099841 object centre at (A) : -1.796500 17.71200 51.33300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9706716 -0.7614810 midg,1,midg; midg,igrid,midg 1.7398750E-02 -0.1552008 1,midg,midg; igrid,midg,midg 8.5827962E-02 0.1744803 gauss-seidel spectral radius is 0.9992975 estimated iterations to convergence 298 setup time was (sec) 2.030000 now iterating at: 17:10:54 rms-change max change #iterations 9.235472 362.9849 at 10iterations 5.427449 130.5913 at 20iterations 3.186655 76.14132 at 30iterations 1.869015 38.25976 at 40iterations 1.093456 21.72293 at 50iterations 0.6408852 12.66508 at 60iterations 0.3729770 6.917966 at 70iterations 0.2181256 4.378410 at 80iterations 0.1268714 2.294567 at 90iterations 7.4061364E-02 1.370495 at 100iterations 4.3200210E-02 0.8319054 at 110iterations 2.5204983E-02 0.5006323 at 120iterations 1.4657166E-02 0.2853050 at 130iterations 8.5268961E-03 0.1488338 at 140iterations 4.9667847E-03 9.5851898E-02 at 150iterations 2.9013392E-03 5.1609039E-02 at 160iterations 1.6897790E-03 3.0125856E-02 at 170iterations 9.8264101E-04 1.7453194E-02 at 180iterations finished qdiffx linear iterations at : 17:11:12 total time elapsed so far: 19.79000 # loops : 180 mean,max change (kT/e) : 9.8264101E-04 1.7453194E-02 energy calculations done at 19.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.96000 DelPhi exited at 17:11:12 19.967u 0.563s 0:20.82 98.5% 0+0k 0+0io 0pf+0w