Tue Oct 11 03:19:50 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 Tue Oct 11 2011 at 03:19:50 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3580 !!! WARNING: GLM 17 has a net charge of -0.0940 !!! WARNING: SEP 228 has a net charge of -0.4750 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: 0.5372450 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): -56.91500 3.197000 ymin,ymax (A): -34.73300 31.53100 zmin,zma (A): -42.77100 11.54700 x,y,z range (A): 60.11200 66.26400 54.31800 scale (grids/A): 0.5372450 object centre (A): -26.85900 -1.601001 -15.61200 number of atom coordinates read : 3580 total number of charged atoms : 3432 net assigned charge : -9.068974 assigned positive charge : 547.8198 centred at (gu) : 87.79821 92.11627 90.94075 assigned negative charge : -556.8907 centred at (gu) : 87.78870 92.10503 90.90289 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6617 nv = 96 ne = 84 npr = 72258 no. pairs analyzed = 72258 no. exposed pairs = 4650 no. arc points = 32443 no. surface atoms = 1548 nbur = 2032 mkacc time = 0.1200000 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 = 1.596000 m= 268 mr = 3361 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3247 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8792 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9203847E-10 -2.1645458E-10 midg,1,midg; midg,igrid,midg -2.7699121E-10 -5.5392724E-10 1,midg,midg; igrid,midg,midg -7.8202417E-10 -2.0115896E-10 gauss-seidel spectral radius is 0.9821864 estimated iterations to convergence 62 setup time was (sec) 0.4600000 now iterating at: 03:19:50 rms-change max change #iterations 7.9841115E-02 17.51199 at 10iterations 5.6462483E-03 0.9093323 at 20iterations 9.0167648E-04 0.1278238 at 30iterations 3.2316279E-04 4.6481133E-02 at 40iterations 1.2605882E-04 1.8451691E-02 at 50iterations finished qdiffx linear iterations at : 03:19:53 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.2605882E-04 1.8451691E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 03:19:54 3.498u 0.164s 0:04.33 84.2% 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 Tue Oct 11 2011 at 03:19:54 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3580 !!! WARNING: GLM 17 has a net charge of -0.0940 !!! WARNING: SEP 228 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.611735 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): -56.91500 3.197000 ymin,ymax (A): -34.73300 31.53100 zmin,zma (A): -42.77100 11.54700 x,y,z range (A): 60.11200 66.26400 54.31800 scale (grids/A): 1.611735 object centre (A): -26.85900 -1.601001 -15.61200 number of atom coordinates read : 3580 total number of charged atoms : 3432 net assigned charge : -9.068974 assigned positive charge : 547.8198 centred at (gu) : 83.39360 96.34798 92.82097 assigned negative charge : -556.8907 centred at (gu) : 83.36522 96.31491 92.70823 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 74020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32443 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 22083 mr = 50027 m= 1993 mr = 14484 m= 46 mr = 826 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 32803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 418 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 26172 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) : 0.5372450 object centre at (A) : -26.85900 -1.601001 -15.61200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2085830E-03 -4.3750661E-03 midg,1,midg; midg,igrid,midg 2.4112327E-02 -1.5551844E-02 1,midg,midg; igrid,midg,midg -1.7074326E-03 -2.5212797E-03 gauss-seidel spectral radius is 0.9981900 estimated iterations to convergence 187 setup time was (sec) 0.5900000 now iterating at: 03:19:55 rms-change max change #iterations 3.653353 175.4547 at 10iterations 1.515013 53.37434 at 20iterations 0.6312911 24.28476 at 30iterations 0.2632949 10.19572 at 40iterations 0.1100633 4.193329 at 50iterations 4.6024255E-02 1.564365 at 60iterations 1.9372422E-02 0.6705241 at 70iterations 8.2710208E-03 0.2869568 at 80iterations 3.6927550E-03 0.1229429 at 90iterations 1.7874856E-03 5.9051514E-02 at 100iterations 9.8414137E-04 3.3943176E-02 at 110iterations 6.2152365E-04 2.0636559E-02 at 120iterations finished qdiffx linear iterations at : 03:20:02 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 6.2152365E-04 2.0636559E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:20:03 7.854u 0.177s 0:08.57 93.5% 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 Tue Oct 11 2011 at 03:20:03 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3580 !!! WARNING: GLM 17 has a net charge of -0.0940 !!! WARNING: SEP 228 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.417602 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): -56.91500 3.197000 ymin,ymax (A): -34.73300 31.53100 zmin,zma (A): -42.77100 11.54700 x,y,z range (A): 60.11200 66.26400 54.31800 scale (grids/A): 2.417602 object centre (A): -26.85900 -1.601001 -15.61200 number of atom coordinates read : 3580 total number of charged atoms : 3432 net assigned charge : -9.068974 assigned positive charge : 547.8198 centred at (gu) : 80.09005 99.52190 94.23122 assigned negative charge : -556.8907 centred at (gu) : 80.04786 99.47218 94.06216 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 172288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32443 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 77821 mr = 123067 m= 20438 mr = 60198 m= 2957 mr = 14635 m= 156 mr = 1700 m= 4 mr = 49 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 0.8800000 number of dielectric boundary points 74015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 27413 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) : 1.611735 object centre at (A) : -26.85900 -1.601001 -15.61200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0616652E-02 -4.6957120E-02 midg,1,midg; midg,igrid,midg 0.5224646 -0.3892616 1,midg,midg; igrid,midg,midg 5.2384451E-02 1.0093885E-02 gauss-seidel spectral radius is 0.9991534 estimated iterations to convergence 271 setup time was (sec) 1.120000 now iterating at: 03:20:04 rms-change max change #iterations 9.668424 337.6548 at 10iterations 5.508237 151.9187 at 20iterations 3.125800 82.51564 at 30iterations 1.758188 41.72127 at 40iterations 0.9831420 23.25847 at 50iterations 0.5510251 12.54824 at 60iterations 0.3069198 7.136108 at 70iterations 0.1709277 3.636690 at 80iterations 9.5163040E-02 2.293719 at 90iterations 5.2821580E-02 1.113060 at 100iterations 2.9364992E-02 0.6634169 at 110iterations 1.6338618E-02 0.3286781 at 120iterations 9.1074789E-03 0.2143207 at 130iterations 5.1154913E-03 0.1118650 at 140iterations 2.9017024E-03 7.0437908E-02 at 150iterations 1.6915945E-03 3.4636974E-02 at 160iterations 1.0291501E-03 2.3303747E-02 at 170iterations 6.6916348E-04 1.6133070E-02 at 180iterations finished qdiffx linear iterations at : 03:20:15 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 6.6916348E-04 1.6133070E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 03:20:16 12.700u 0.220s 0:13.23 97.6% 0+0k 0+0io 0pf+0w