Sun Oct 9 11:35:26 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 11:35:26 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 = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6992046 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): -16.87900 34.03600 ymin,ymax (A): -20.15100 28.29200 zmin,zma (A): 16.94800 66.68600 x,y,z range (A): 50.91500 48.44300 49.73800 scale (grids/A): 0.6992046 object centre (A): 8.578500 4.070500 41.81700 number of atom coordinates read : 1956 total number of charged atoms : 1819 net assigned charge : 2.500010 assigned positive charge : 281.2270 centred at (gu) : 89.93298 88.81317 89.34458 assigned negative charge : -278.7274 centred at (gu) : 89.87685 88.73891 89.40763 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6770 nv = 96 ne = 84 npr = 39197 no. pairs analyzed = 39197 no. exposed pairs = 2727 no. arc points = 18850 no. surface atoms = 921 nbur = 1035 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 3515 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 3656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1571 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7195 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6064280E-08 -4.8872808E-09 midg,1,midg; midg,igrid,midg -1.2887136E-08 3.5292800E-08 1,midg,midg; igrid,midg,midg -3.2058065E-09 3.7473399E-08 gauss-seidel spectral radius is 0.9893451 estimated iterations to convergence 79 setup time was (sec) 0.3400000 now iterating at: 11:35:27 rms-change max change #iterations 0.1735259 27.08462 at 10iterations 2.0834563E-02 2.765928 at 20iterations 2.5135670E-03 0.3771334 at 30iterations 3.0375973E-04 4.3385029E-02 at 40iterations 3.8237871E-05 6.2284470E-03 at 50iterations finished qdiffx linear iterations at : 11:35:29 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.8237871E-05 6.2284470E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 11:35:30 3.411u 0.190s 0:03.92 91.8% 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 Sun Oct 9 2011 at 11:35:30 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 = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.097614 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): -16.87900 34.03600 ymin,ymax (A): -20.15100 28.29200 zmin,zma (A): 16.94800 66.68600 x,y,z range (A): 50.91500 48.44300 49.73800 scale (grids/A): 2.097614 object centre (A): 8.578500 4.070500 41.81700 number of atom coordinates read : 1956 total number of charged atoms : 1819 net assigned charge : 2.500010 assigned positive charge : 281.2270 centred at (gu) : 89.79889 86.43955 88.03386 assigned negative charge : -278.7274 centred at (gu) : 89.63069 86.21703 88.22324 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18850 grid for indexing accessible points = 1.400000 m= 27290 mr = 47281 m= 5764 mr = 19801 m= 574 mr = 3797 m= 19 mr = 281 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 33559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 14456 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) : 0.6992046 object centre at (A) : 8.578500 4.070500 41.81700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8403942E-02 -6.1458140E-04 midg,1,midg; midg,igrid,midg 2.7257092E-02 3.2661099E-02 1,midg,midg; igrid,midg,midg -3.4985043E-02 -1.9136500E-02 gauss-seidel spectral radius is 0.9988120 estimated iterations to convergence 230 setup time was (sec) 0.6000000 now iterating at: 11:35:31 rms-change max change #iterations 4.298148 232.9471 at 10iterations 2.103849 73.13385 at 20iterations 1.041216 30.46243 at 30iterations 0.5125829 17.49054 at 40iterations 0.2531164 8.016651 at 50iterations 0.1250741 3.749587 at 60iterations 6.1735488E-02 1.978903 at 70iterations 3.0383304E-02 1.009068 at 80iterations 1.5047638E-02 0.4729853 at 90iterations 7.3733376E-03 0.2452698 at 100iterations 3.6411141E-03 0.1168008 at 110iterations 1.7971857E-03 5.6514025E-02 at 120iterations finished qdiffx linear iterations at : 11:35:38 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.7971857E-03 5.6514025E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 11:35:38 7.904u 0.208s 0:08.44 95.9% 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 Sun Oct 9 2011 at 11:35:38 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 = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.146420 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): -16.87900 34.03600 ymin,ymax (A): -20.15100 28.29200 zmin,zma (A): 16.94800 66.68600 x,y,z range (A): 50.91500 48.44300 49.73800 scale (grids/A): 3.146420 object centre (A): 8.578500 4.070500 41.81700 number of atom coordinates read : 1956 total number of charged atoms : 1819 net assigned charge : 2.500010 assigned positive charge : 281.2270 centred at (gu) : 89.69836 84.65933 87.05083 assigned negative charge : -278.7274 centred at (gu) : 89.44611 84.32548 87.33490 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 163974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18850 grid for indexing accessible points = 1.400000 m= 83259 mr = 114866 m= 35323 mr = 66899 m= 11002 mr = 28463 m= 2238 mr = 8464 m= 270 mr = 1596 m= 13 mr = 157 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 75632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 14552 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) : 2.097614 object centre at (A) : 8.578500 4.070500 41.81700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1177363 -9.3673304E-02 midg,1,midg; midg,igrid,midg 0.3306648 0.3056090 1,midg,midg; igrid,midg,midg -9.5923163E-02 -0.2392942 gauss-seidel spectral radius is 0.9993054 estimated iterations to convergence 299 setup time was (sec) 1.350000 now iterating at: 11:35:40 rms-change max change #iterations 9.631932 408.4033 at 10iterations 5.696311 160.5385 at 20iterations 3.364786 80.39754 at 30iterations 1.993049 36.67314 at 40iterations 1.176860 25.87166 at 50iterations 0.6919288 13.64133 at 60iterations 0.4072245 7.606226 at 70iterations 0.2387989 4.089986 at 80iterations 0.1403410 2.509472 at 90iterations 8.2294427E-02 1.416336 at 100iterations 4.8112437E-02 0.9628913 at 110iterations 2.8166834E-02 0.5009966 at 120iterations 1.6543014E-02 0.3026295 at 130iterations 9.6711200E-03 0.1784620 at 140iterations 5.6586266E-03 0.1016579 at 150iterations 3.3188090E-03 6.0329437E-02 at 160iterations 1.9420100E-03 3.5308838E-02 at 170iterations 1.1398176E-03 2.1092415E-02 at 180iterations finished qdiffx linear iterations at : 11:35:51 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 1.1398176E-03 2.1092415E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 11:35:52 12.923u 0.206s 0:13.40 97.9% 0+0k 0+0io 0pf+0w