Sat Oct 8 19:09:31 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 Sat Oct 8 2011 at 19:09:31 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 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: 0.6485817 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): -31.70200 17.45500 ymin,ymax (A): -21.36500 23.01200 zmin,zma (A): -12.65400 42.23500 x,y,z range (A): 49.15700 44.37700 54.88900 scale (grids/A): 0.6485817 object centre (A): -7.123500 0.8234997 14.79050 number of atom coordinates read : 2424 total number of charged atoms : 2285 net assigned charge : 6.000006 assigned positive charge : 363.0873 centred at (gu) : 88.67030 89.09822 90.20637 assigned negative charge : -357.0877 centred at (gu) : 88.57371 89.23117 90.12971 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6821 nv = 96 ne = 84 npr = 50552 no. pairs analyzed = 50552 no. exposed pairs = 2778 no. arc points = 20145 no. surface atoms = 934 nbur = 1490 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 3910 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 201 time to turn everything in is 0.2800000 number of dielectric boundary points 3216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1938 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8137 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9963085E-10 2.2323302E-08 midg,1,midg; midg,igrid,midg 3.4873835E-08 -5.7192069E-09 1,midg,midg; igrid,midg,midg -2.9559666E-09 1.8201145E-08 gauss-seidel spectral radius is 0.9876635 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 19:09:31 rms-change max change #iterations 0.1509713 23.93356 at 10iterations 1.5324305E-02 2.141012 at 20iterations 1.5487187E-03 0.2180328 at 30iterations 1.6110593E-04 2.3613930E-02 at 40iterations 1.6568041E-05 2.3822784E-03 at 50iterations finished qdiffx linear iterations at : 19:09:35 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.6568041E-05 2.3822784E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 19:09:35 4.189u 0.232s 0:04.70 93.8% 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 Sat Oct 8 2011 at 19:09:35 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 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: 1.945745 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): -31.70200 17.45500 ymin,ymax (A): -21.36500 23.01200 zmin,zma (A): -12.65400 42.23500 x,y,z range (A): 49.15700 44.37700 54.88900 scale (grids/A): 1.945745 object centre (A): -7.123500 0.8234997 14.79050 number of atom coordinates read : 2424 total number of charged atoms : 2285 net assigned charge : 6.000006 assigned positive charge : 363.0873 centred at (gu) : 86.01048 87.29449 90.61900 assigned negative charge : -357.0877 centred at (gu) : 85.72103 87.69332 90.38889 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20145 grid for indexing accessible points = 1.400000 m= 27799 mr = 52280 m= 4666 mr = 21287 m= 305 mr = 3109 m= 4 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 8432 time to turn everything in is 0.5700000 number of dielectric boundary points 29791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18003 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) : 0.6485817 object centre at (A) : -7.123500 0.8234997 14.79050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6955970E-02 1.3711005E-02 midg,1,midg; midg,igrid,midg 4.8679005E-02 9.4535435E-04 1,midg,midg; igrid,midg,midg -5.3772639E-04 4.1526560E-02 gauss-seidel spectral radius is 0.9986696 estimated iterations to convergence 217 setup time was (sec) 0.9100000 now iterating at: 19:09:37 rms-change max change #iterations 4.197070 186.5090 at 10iterations 1.991695 70.51446 at 20iterations 0.9413146 29.22809 at 30iterations 0.4457651 15.11125 at 40iterations 0.2108409 6.802353 at 50iterations 9.9714264E-02 3.158484 at 60iterations 4.7068655E-02 1.477036 at 70iterations 2.2350516E-02 0.7292557 at 80iterations 1.0555740E-02 0.3197670 at 90iterations 4.9979081E-03 0.1493263 at 100iterations 2.3654995E-03 7.3258400E-02 at 110iterations 1.1191869E-03 3.2943726E-02 at 120iterations finished qdiffx linear iterations at : 19:09:45 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 1.1191869E-03 3.2943726E-02 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.920000 DelPhi exited at 19:09:46 9.925u 0.327s 0:10.54 97.1% 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 Sat Oct 8 2011 at 19:09:46 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 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: 2.918617 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): -31.70200 17.45500 ymin,ymax (A): -21.36500 23.01200 zmin,zma (A): -12.65400 42.23500 x,y,z range (A): 49.15700 44.37700 54.88900 scale (grids/A): 2.918617 object centre (A): -7.123500 0.8234997 14.79050 number of atom coordinates read : 2424 total number of charged atoms : 2285 net assigned charge : 6.000006 assigned positive charge : 363.0873 centred at (gu) : 84.01572 85.94161 90.92845 assigned negative charge : -357.0877 centred at (gu) : 83.58153 86.53998 90.58325 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 170328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20145 grid for indexing accessible points = 1.400000 m= 89147 mr = 125605 m= 33663 mr = 74902 m= 8593 mr = 27913 m= 1440 mr = 6706 m= 100 mr = 1060 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 28469 time to turn everything in is 1.480000 number of dielectric boundary points 67039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 18279 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) : 1.945745 object centre at (A) : -7.123500 0.8234997 14.79050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3413767E-02 0.2635102 midg,1,midg; midg,igrid,midg 0.4807287 2.1073157E-03 1,midg,midg; igrid,midg,midg 5.3376671E-02 0.4391339 gauss-seidel spectral radius is 0.9992588 estimated iterations to convergence 290 setup time was (sec) 1.870000 now iterating at: 19:09:48 rms-change max change #iterations 9.692057 465.9703 at 10iterations 5.559122 109.7996 at 20iterations 3.181684 56.78474 at 30iterations 1.822098 35.34269 at 40iterations 1.044399 19.82512 at 50iterations 0.5986350 10.34679 at 60iterations 0.3432038 5.785307 at 70iterations 0.1964539 3.453705 at 80iterations 0.1126867 2.091995 at 90iterations 6.4471200E-02 1.159376 at 100iterations 3.6923625E-02 0.6723671 at 110iterations 2.1192500E-02 0.3824692 at 120iterations 1.2158161E-02 0.2283936 at 130iterations 6.9728806E-03 0.1221867 at 140iterations 3.9938069E-03 7.6660156E-02 at 150iterations 2.2902349E-03 4.0035248E-02 at 160iterations 1.3159991E-03 2.6912689E-02 at 170iterations 7.5455423E-04 1.3415337E-02 at 180iterations finished qdiffx linear iterations at : 19:10:02 total time elapsed so far: 15.87000 # loops : 180 mean,max change (kT/e) : 7.5455423E-04 1.3415337E-02 energy calculations done at 15.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.06000 DelPhi exited at 19:10:03 16.061u 0.326s 0:16.66 98.3% 0+0k 0+0io 0pf+0w