Sun Oct 9 22:31:42 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 Sun Oct 9 2011 at 22:31:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6213240 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): 3.520000 54.61800 ymin,ymax (A): 17.47200 74.76900 zmin,zma (A): 59.23200 112.9300 x,y,z range (A): 51.09800 57.29700 53.69800 scale (grids/A): 0.6213240 object centre (A): 29.06900 46.12050 86.08100 number of atom coordinates read : 3026 total number of charged atoms : 2931 net assigned charge : 5.000019 assigned positive charge : 467.5159 centred at (gu) : 89.18073 90.49658 89.54951 assigned negative charge : -462.5170 centred at (gu) : 89.19653 90.47985 89.66309 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8037 nv = 96 ne = 84 npr = 56314 no. pairs analyzed = 56314 no. exposed pairs = 4240 no. arc points = 30730 no. surface atoms = 1404 nbur = 1622 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 3974 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3400000 number of dielectric boundary points 4467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3050 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9868 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4750523E-08 -4.8062607E-09 midg,1,midg; midg,igrid,midg 2.4803430E-09 6.1225864E-09 1,midg,midg; igrid,midg,midg 6.4753642E-09 2.3853650E-09 gauss-seidel spectral radius is 0.9866410 estimated iterations to convergence 71 setup time was (sec) 0.5700000 now iterating at: 22:31:43 rms-change max change #iterations 0.1348831 21.09231 at 10iterations 1.2636984E-02 1.771362 at 20iterations 1.1637893E-03 0.1872005 at 30iterations 1.1224454E-04 1.6082764E-02 at 40iterations 1.3500520E-05 1.6555786E-03 at 50iterations finished qdiffx linear iterations at : 22:31:46 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.3500520E-05 1.6555786E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 22:31:46 3.420u 0.145s 0:03.84 92.7% 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 22:31:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.863972 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): 3.520000 54.61800 ymin,ymax (A): 17.47200 74.76900 zmin,zma (A): 59.23200 112.9300 x,y,z range (A): 51.09800 57.29700 53.69800 scale (grids/A): 1.863972 object centre (A): 29.06900 46.12050 86.08100 number of atom coordinates read : 3026 total number of charged atoms : 2931 net assigned charge : 5.000019 assigned positive charge : 467.5159 centred at (gu) : 87.54110 91.48917 88.64809 assigned negative charge : -462.5170 centred at (gu) : 87.58940 91.43899 88.98867 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30730 grid for indexing accessible points = 1.400000 m= 29302 mr = 55601 m= 4383 mr = 20361 m= 258 mr = 2487 m= 1 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 287 time to turn everything in is 0.6300000 number of dielectric boundary points 41373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22970 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) : 0.6213240 object centre at (A) : 29.06900 46.12050 86.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2353856E-02 -1.0707525E-02 midg,1,midg; midg,igrid,midg 3.0276004E-02 -1.2857481E-02 1,midg,midg; igrid,midg,midg 1.7756958E-02 1.8114092E-02 gauss-seidel spectral radius is 0.9986557 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 22:31:47 rms-change max change #iterations 4.498793 181.3429 at 10iterations 2.105494 68.09537 at 20iterations 0.9876022 31.29134 at 30iterations 0.4617833 13.77415 at 40iterations 0.2166853 7.134531 at 50iterations 0.1019570 3.208374 at 60iterations 4.7835529E-02 1.549978 at 70iterations 2.2487652E-02 0.6828232 at 80iterations 1.0568192E-02 0.3206539 at 90iterations 4.9811341E-03 0.1487885 at 100iterations 2.3430549E-03 8.4247589E-02 at 110iterations 1.1031923E-03 3.4034729E-02 at 120iterations finished qdiffx linear iterations at : 22:31:54 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 1.1031923E-03 3.4034729E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 22:31:55 8.124u 0.151s 0:08.64 95.7% 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 22:31:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.795958 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): 3.520000 54.61800 ymin,ymax (A): 17.47200 74.76900 zmin,zma (A): 59.23200 112.9300 x,y,z range (A): 51.09800 57.29700 53.69800 scale (grids/A): 2.795958 object centre (A): 29.06900 46.12050 86.08100 number of atom coordinates read : 3026 total number of charged atoms : 2931 net assigned charge : 5.000019 assigned positive charge : 467.5159 centred at (gu) : 86.31151 92.23353 87.97188 assigned negative charge : -462.5170 centred at (gu) : 86.38399 92.15836 88.48302 start vw surface at 0.2000000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 198282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30730 grid for indexing accessible points = 1.400000 m= 95588 mr = 135677 m= 32951 mr = 75239 m= 7586 mr = 25158 m= 1023 mr = 5323 m= 70 mr = 712 m= 0 mr = 18 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1026 time to turn everything in is 1.600000 number of dielectric boundary points 93373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 23443 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) : 1.863972 object centre at (A) : 29.06900 46.12050 86.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2921653 -0.1268166 midg,1,midg; midg,igrid,midg 0.3417618 -0.2689956 1,midg,midg; igrid,midg,midg 0.1583246 0.2776653 gauss-seidel spectral radius is 0.9993008 estimated iterations to convergence 298 setup time was (sec) 1.910000 now iterating at: 22:31:57 rms-change max change #iterations 10.87419 310.5906 at 10iterations 6.622624 158.9330 at 20iterations 3.977089 103.3202 at 30iterations 2.377187 51.50328 at 40iterations 1.416722 32.76201 at 50iterations 0.8393397 15.56372 at 60iterations 0.4972161 9.285192 at 70iterations 0.2931596 5.131975 at 80iterations 0.1725860 3.236229 at 90iterations 0.1016368 1.891461 at 100iterations 5.9670925E-02 1.059752 at 110iterations 3.5028499E-02 0.6422729 at 120iterations 2.0568527E-02 0.3490162 at 130iterations 1.2086898E-02 0.2217560 at 140iterations 7.0791165E-03 0.1501274 at 150iterations 4.1369651E-03 7.7610016E-02 at 160iterations 2.4219684E-03 4.5835495E-02 at 170iterations 1.4180590E-03 2.4803162E-02 at 180iterations finished qdiffx linear iterations at : 22:32:08 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 1.4180590E-03 2.4803162E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 22:32:08 12.492u 0.197s 0:13.06 97.0% 0+0k 0+0io 0pf+0w