Tue Oct 11 06:27:50 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 06:27:51 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2052 !!! WARNING: HIR 46 has a net charge of 0.5140 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 0.6969596 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): -27.30900 13.57300 ymin,ymax (A): 20.24700 65.09600 zmin,zma (A): -17.76100 33.31800 x,y,z range (A): 40.88200 44.84900 51.07900 scale (grids/A): 0.6969596 object centre (A): -6.868000 42.67150 7.778501 number of atom coordinates read : 2052 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.1080 centred at (gu) : 89.10715 90.20361 91.10735 assigned negative charge : -311.1631 centred at (gu) : 89.06209 90.34711 91.15652 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6797 nv = 96 ne = 84 npr = 40654 no. pairs analyzed = 40654 no. exposed pairs = 2502 no. arc points = 17221 no. surface atoms = 858 nbur = 1194 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3860 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1648 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7637 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7254755E-08 2.4856451E-08 midg,1,midg; midg,igrid,midg 9.0719674E-08 -1.7803750E-08 1,midg,midg; igrid,midg,midg 2.5839521E-08 4.7921880E-08 gauss-seidel spectral radius is 0.9892683 estimated iterations to convergence 79 setup time was (sec) 0.4900000 now iterating at: 06:27:51 rms-change max change #iterations 0.1888458 26.04310 at 10iterations 2.2871859E-02 3.412750 at 20iterations 3.0544116E-03 0.3968887 at 30iterations 5.2437547E-04 6.6177368E-02 at 40iterations 1.2356385E-04 1.5319824E-02 at 50iterations finished qdiffx linear iterations at : 06:27:54 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.2356385E-04 1.5319824E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 06:27:55 3.260u 0.191s 0:03.99 86.4% 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 Tue Oct 11 2011 at 06:27:55 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2052 !!! WARNING: HIR 46 has a net charge of 0.5140 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 2.090879 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): -27.30900 13.57300 ymin,ymax (A): 20.24700 65.09600 zmin,zma (A): -17.76100 33.31800 x,y,z range (A): 40.88200 44.84900 51.07900 scale (grids/A): 2.090879 object centre (A): -6.868000 42.67150 7.778501 number of atom coordinates read : 2052 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.1080 centred at (gu) : 87.32155 90.61111 93.32203 assigned negative charge : -311.1631 centred at (gu) : 87.18650 91.04150 93.46975 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17221 grid for indexing accessible points = 1.400000 m= 28171 mr = 50696 m= 5292 mr = 21169 m= 428 mr = 3440 m= 20 mr = 192 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 539 time to turn everything in is 0.5300000 number of dielectric boundary points 30202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15382 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) : 0.6969596 object centre at (A) : -6.868000 42.67150 7.778501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8962135E-02 4.5972854E-02 midg,1,midg; midg,igrid,midg 3.5897382E-02 4.5985309E-03 1,midg,midg; igrid,midg,midg 2.0490499E-02 1.1262801E-02 gauss-seidel spectral radius is 0.9987972 estimated iterations to convergence 228 setup time was (sec) 0.8100000 now iterating at: 06:27:56 rms-change max change #iterations 4.518480 218.9428 at 10iterations 2.218996 80.27789 at 20iterations 1.093503 37.29112 at 30iterations 0.5389063 17.48614 at 40iterations 0.2648722 8.534637 at 50iterations 0.1306507 4.073151 at 60iterations 6.4169362E-02 1.854313 at 70iterations 3.1530280E-02 0.9990501 at 80iterations 1.5649443E-02 0.5194778 at 90iterations 7.7347574E-03 0.2283289 at 100iterations 3.8412807E-03 0.1226749 at 110iterations 1.9412579E-03 6.1817169E-02 at 120iterations finished qdiffx linear iterations at : 06:28:02 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 1.9412579E-03 6.1817169E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 06:28:03 7.378u 0.231s 0:08.09 93.9% 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 Tue Oct 11 2011 at 06:28:03 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2052 !!! WARNING: HIR 46 has a net charge of 0.5140 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.136318 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): -27.30900 13.57300 ymin,ymax (A): 20.24700 65.09600 zmin,zma (A): -17.76100 33.31800 x,y,z range (A): 40.88200 44.84900 51.07900 scale (grids/A): 3.136318 object centre (A): -6.868000 42.67150 7.778501 number of atom coordinates read : 2052 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.1080 centred at (gu) : 85.98234 90.91677 94.98299 assigned negative charge : -311.1631 centred at (gu) : 85.77971 91.56226 95.20454 start vw surface at 0.1200000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 165216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17221 grid for indexing accessible points = 1.400000 m= 88905 mr = 122239 m= 34924 mr = 73455 m= 9832 mr = 28359 m= 1928 mr = 7594 m= 224 mr = 1383 m= 12 mr = 131 m= 0 mr = 1 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1680 time to turn everything in is 1.640000 number of dielectric boundary points 67879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 15504 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) : 2.090879 object centre at (A) : -6.868000 42.67150 7.778501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3798203 0.3634590 midg,1,midg; midg,igrid,midg 0.2795350 4.9907856E-02 1,midg,midg; igrid,midg,midg 0.2819141 7.3483676E-02 gauss-seidel spectral radius is 0.9992878 estimated iterations to convergence 296 setup time was (sec) 1.930000 now iterating at: 06:28:05 rms-change max change #iterations 10.17679 331.1817 at 10iterations 6.007764 130.1235 at 20iterations 3.544743 74.17690 at 30iterations 2.082452 51.57928 at 40iterations 1.222734 25.00623 at 50iterations 0.7168438 14.65871 at 60iterations 0.4183940 7.660469 at 70iterations 0.2443461 4.704000 at 80iterations 0.1426486 2.947039 at 90iterations 8.3375961E-02 1.742287 at 100iterations 4.8828039E-02 0.9515615 at 110iterations 2.8550461E-02 0.5135403 at 120iterations 1.6757630E-02 0.2920189 at 130iterations 9.8805856E-03 0.1715698 at 140iterations 5.8856821E-03 0.1157379 at 150iterations 3.5601694E-03 6.9664001E-02 at 160iterations 2.2385896E-03 4.3579102E-02 at 170iterations 1.4693509E-03 2.9098511E-02 at 180iterations finished qdiffx linear iterations at : 06:28:16 total time elapsed so far: 13.31000 # loops : 180 mean,max change (kT/e) : 1.4693509E-03 2.9098511E-02 energy calculations done at 13.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 06:28:17 13.480u 0.239s 0:14.38 95.3% 0+0k 0+0io 0pf+0w