Sun Oct 9 22:12:08 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 Sun Oct 9 2011 at 22:12:08 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 = 2576 !!! WARNING: SEP 139 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6353966 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): -9.044000 45.88100 ymin,ymax (A): -16.49500 39.53300 zmin,zma (A): -3.814000 49.19000 x,y,z range (A): 54.92500 56.02800 53.00400 scale (grids/A): 0.6353966 object centre (A): 18.41850 11.51900 22.68800 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.4179 centred at (gu) : 91.18063 90.18471 90.21197 assigned negative charge : -385.8936 centred at (gu) : 91.25145 90.15705 90.23270 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6762 nv = 96 ne = 84 npr = 52504 no. pairs analyzed = 52504 no. exposed pairs = 3129 no. arc points = 22117 no. surface atoms = 1058 nbur = 1518 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3635 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.2000000 number of dielectric boundary points 3425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2272 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8388 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6205824E-09 3.8993773E-09 midg,1,midg; midg,igrid,midg 2.9172254E-09 9.0186614E-09 1,midg,midg; igrid,midg,midg 1.0134800E-08 -1.9622419E-09 gauss-seidel spectral radius is 0.9871660 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 22:12:08 rms-change max change #iterations 0.1397810 20.84644 at 10iterations 1.3801992E-02 2.128961 at 20iterations 1.3306770E-03 0.1883678 at 30iterations 1.3174737E-04 1.7973185E-02 at 40iterations 1.2705662E-05 1.7738342E-03 at 50iterations finished qdiffx linear iterations at : 22:12:11 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.2705662E-05 1.7738342E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 22:12:11 3.408u 0.179s 0:03.87 92.2% 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 Sun Oct 9 2011 at 22:12:12 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 = 2576 !!! WARNING: SEP 139 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.906190 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): -9.044000 45.88100 ymin,ymax (A): -16.49500 39.53300 zmin,zma (A): -3.814000 49.19000 x,y,z range (A): 54.92500 56.02800 53.00400 scale (grids/A): 1.906190 object centre (A): 18.41850 11.51900 22.68800 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.4179 centred at (gu) : 93.54154 90.55412 90.63554 assigned negative charge : -385.8936 centred at (gu) : 93.75423 90.47107 90.69795 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22117 grid for indexing accessible points = 1.400000 m= 24373 mr = 50499 m= 3524 mr = 17472 m= 228 mr = 2139 m= 3 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2381 time to turn everything in is 0.3600000 number of dielectric boundary points 31677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19139 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) : 0.6353966 object centre at (A) : 18.41850 11.51900 22.68800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7719432E-02 -8.4163779E-03 midg,1,midg; midg,igrid,midg 2.1345362E-02 -2.4855521E-03 1,midg,midg; igrid,midg,midg -5.4150806E-03 1.7852850E-02 gauss-seidel spectral radius is 0.9986286 estimated iterations to convergence 214 setup time was (sec) 0.5800000 now iterating at: 22:12:12 rms-change max change #iterations 4.207375 177.9979 at 10iterations 1.972058 64.31244 at 20iterations 0.9212188 33.14991 at 30iterations 0.4288689 13.94350 at 40iterations 0.2004389 6.894104 at 50iterations 9.3753733E-02 2.938820 at 60iterations 4.3720666E-02 1.413124 at 70iterations 2.0484848E-02 0.7315788 at 80iterations 9.5742792E-03 0.2898602 at 90iterations 4.4744089E-03 0.1510382 at 100iterations 2.0876396E-03 6.5945625E-02 at 110iterations 9.7353669E-04 3.0660629E-02 at 120iterations finished qdiffx linear iterations at : 22:12:19 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 9.7353669E-04 3.0660629E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 22:12:20 7.848u 0.182s 0:08.35 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 Sun Oct 9 2011 at 22:12:20 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 = 2576 !!! WARNING: SEP 139 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.859285 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): -9.044000 45.88100 ymin,ymax (A): -16.49500 39.53300 zmin,zma (A): -3.814000 49.19000 x,y,z range (A): 54.92500 56.02800 53.00400 scale (grids/A): 2.859285 object centre (A): 18.41850 11.51900 22.68800 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.4179 centred at (gu) : 95.31224 90.83091 90.95300 assigned negative charge : -385.8936 centred at (gu) : 95.63110 90.70649 91.04693 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 170754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22117 grid for indexing accessible points = 1.400000 m= 81536 mr = 122721 m= 26697 mr = 65957 m= 6293 mr = 20861 m= 1011 mr = 4619 m= 65 mr = 765 m= 0 mr = 25 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 8008 time to turn everything in is 0.9200000 number of dielectric boundary points 71408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19438 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) : 1.906190 object centre at (A) : 18.41850 11.51900 22.68800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4165087 -0.2558787 midg,1,midg; midg,igrid,midg 0.2070226 4.2097598E-02 1,midg,midg; igrid,midg,midg -0.2173235 0.2129791 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 1.160000 now iterating at: 22:12:21 rms-change max change #iterations 9.917991 336.9091 at 10iterations 5.760054 120.4993 at 20iterations 3.321339 65.98962 at 30iterations 1.913313 37.45015 at 40iterations 1.099859 21.31105 at 50iterations 0.6311315 11.89384 at 60iterations 0.3618151 6.858531 at 70iterations 0.2076712 3.751410 at 80iterations 0.1190943 2.240868 at 90iterations 6.8205990E-02 1.214368 at 100iterations 3.9109655E-02 0.6805801 at 110iterations 2.2408653E-02 0.4359207 at 120iterations 1.2854006E-02 0.2631149 at 130iterations 7.3641012E-03 0.1275187 at 140iterations 4.2189602E-03 7.4707747E-02 at 150iterations 2.4178806E-03 4.2309046E-02 at 160iterations 1.3853870E-03 2.4887085E-02 at 170iterations 7.9498300E-04 1.5777588E-02 at 180iterations finished qdiffx linear iterations at : 22:12:33 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 7.9498300E-04 1.5777588E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 22:12:33 12.653u 0.209s 0:13.13 97.8% 0+0k 0+0io 0pf+0w