Sat Oct 15 12:55:16 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 Sat Oct 15 2011 at 12:55:16 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2906 !!! WARNING: HIR 203 has a net charge of 0.5140 !!! WARNING: CME 304 has a net charge of -0.3480 !!! WARNING: CME 446 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 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: 0.5797762 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): -22.36700 39.03600 ymin,ymax (A): -25.02600 29.29400 zmin,zma (A): -30.21500 27.37000 x,y,z range (A): 61.40300 54.32000 57.58500 scale (grids/A): 0.5797762 object centre (A): 8.334499 2.134001 -1.422500 number of atom coordinates read : 2906 total number of charged atoms : 2783 net assigned charge : 0.7130345 assigned positive charge : 428.8550 centred at (gu) : 89.55025 89.58778 91.58808 assigned negative charge : -428.1438 centred at (gu) : 89.57141 89.63966 91.58425 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6730 nv = 96 ne = 84 npr = 56612 no. pairs analyzed = 56612 no. exposed pairs = 4082 no. arc points = 29153 no. surface atoms = 1352 nbur = 1554 mkacc time = 0.1300000 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= 340 mr = 3299 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3300000 number of dielectric boundary points 3746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2849 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8418 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6655665E-11 3.2668399E-10 midg,1,midg; midg,igrid,midg 1.3539386E-09 -8.6079466E-10 1,midg,midg; igrid,midg,midg 6.5427225E-10 -2.6861421E-10 gauss-seidel spectral radius is 0.9846559 estimated iterations to convergence 66 setup time was (sec) 0.6000000 now iterating at: 12:55:17 rms-change max change #iterations 9.5980495E-02 15.18882 at 10iterations 7.9921791E-03 1.360100 at 20iterations 1.1176817E-03 0.1984310 at 30iterations 3.0422187E-04 5.6863785E-02 at 40iterations 9.3130744E-05 1.7551422E-02 at 50iterations finished qdiffx linear iterations at : 12:55:21 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 9.3130744E-05 1.7551422E-02 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 12:55:21 4.319u 0.276s 0:04.90 93.4% 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 Sat Oct 15 2011 at 12:55:21 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2906 !!! WARNING: HIR 203 has a net charge of 0.5140 !!! WARNING: CME 304 has a net charge of -0.3480 !!! WARNING: CME 446 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 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: 1.739329 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): -22.36700 39.03600 ymin,ymax (A): -25.02600 29.29400 zmin,zma (A): -30.21500 27.37000 x,y,z range (A): 61.40300 54.32000 57.58500 scale (grids/A): 1.739329 object centre (A): 8.334499 2.134001 -1.422500 number of atom coordinates read : 2906 total number of charged atoms : 2783 net assigned charge : 0.7130345 assigned positive charge : 428.8550 centred at (gu) : 88.64999 88.76231 94.76311 assigned negative charge : -428.1438 centred at (gu) : 88.71398 88.91907 94.75266 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73452 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29153 grid for indexing accessible points = 1.400000 m= 23763 mr = 48223 m= 3289 mr = 15929 m= 136 mr = 1748 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1382 time to turn everything in is 0.5600000 number of dielectric boundary points 34723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21672 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) : 0.5797762 object centre at (A) : 8.334499 2.134001 -1.422500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9800430E-03 2.1833382E-03 midg,1,midg; midg,igrid,midg 1.1789498E-02 7.1334620E-03 1,midg,midg; igrid,midg,midg 8.7038716E-03 -2.8646899E-02 gauss-seidel spectral radius is 0.9984267 estimated iterations to convergence 200 setup time was (sec) 0.8900000 now iterating at: 12:55:22 rms-change max change #iterations 3.726178 174.1471 at 10iterations 1.632344 55.36250 at 20iterations 0.7210637 26.94506 at 30iterations 0.3190714 11.62865 at 40iterations 0.1410629 4.619610 at 50iterations 6.2450424E-02 2.051910 at 60iterations 2.7791115E-02 0.9319344 at 70iterations 1.2416533E-02 0.4223726 at 80iterations 5.6247395E-03 0.1971130 at 90iterations 2.6069439E-03 9.0557098E-02 at 100iterations 1.2679471E-03 4.7065735E-02 at 110iterations 6.6523219E-04 2.5279999E-02 at 120iterations finished qdiffx linear iterations at : 12:55:31 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 6.6523219E-04 2.5279999E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.930000 DelPhi exited at 12:55:32 9.937u 0.299s 0:10.64 96.0% 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 Sat Oct 15 2011 at 12:55:32 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2906 !!! WARNING: HIR 203 has a net charge of 0.5140 !!! WARNING: CME 304 has a net charge of -0.3480 !!! WARNING: CME 446 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 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: 2.608993 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): -22.36700 39.03600 ymin,ymax (A): -25.02600 29.29400 zmin,zma (A): -30.21500 27.37000 x,y,z range (A): 61.40300 54.32000 57.58500 scale (grids/A): 2.608993 object centre (A): 8.334499 2.134001 -1.422500 number of atom coordinates read : 2906 total number of charged atoms : 2783 net assigned charge : 0.7130345 assigned positive charge : 428.8550 centred at (gu) : 87.97478 88.14324 97.14431 assigned negative charge : -428.1438 centred at (gu) : 88.07113 88.37856 97.12911 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 170466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29153 grid for indexing accessible points = 1.400000 m= 78486 mr = 118785 m= 25733 mr = 60608 m= 5602 mr = 19101 m= 606 mr = 3738 m= 11 mr = 332 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 4583 time to turn everything in is 1.390000 number of dielectric boundary points 78340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 22253 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) : 1.739329 object centre at (A) : 8.334499 2.134001 -1.422500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1082779 7.9827391E-02 midg,1,midg; midg,igrid,midg 0.2191204 0.1555507 1,midg,midg; igrid,midg,midg 0.1925151 -0.7129856 gauss-seidel spectral radius is 0.9992166 estimated iterations to convergence 282 setup time was (sec) 1.760000 now iterating at: 12:55:34 rms-change max change #iterations 9.446858 321.4561 at 10iterations 5.518329 134.3338 at 20iterations 3.181057 70.48526 at 30iterations 1.832025 40.80471 at 40iterations 1.050191 22.87836 at 50iterations 0.6009344 13.28803 at 60iterations 0.3419789 7.173925 at 70iterations 0.1951057 3.873871 at 80iterations 0.1108529 2.318466 at 90iterations 6.2941037E-02 1.197800 at 100iterations 3.5663720E-02 0.6742210 at 110iterations 2.0222384E-02 0.3745890 at 120iterations 1.1504405E-02 0.2247925 at 130iterations 6.5388680E-03 0.1434326 at 140iterations 3.7384909E-03 8.2662582E-02 at 150iterations 2.1563831E-03 4.1561127E-02 at 160iterations 1.2663997E-03 2.7095795E-02 at 170iterations 7.6248730E-04 1.7520905E-02 at 180iterations finished qdiffx linear iterations at : 12:55:48 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 7.6248730E-04 1.7520905E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.28000 DelPhi exited at 12:55:49 16.281u 0.301s 0:16.98 97.6% 0+0k 0+0io 0pf+0w