Sat Oct 8 12:23:44 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 12:23:44 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 = 3021 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5090004 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): -60.11600 9.825000 ymin,ymax (A): -37.87400 17.89900 zmin,zma (A): -4.446000 56.94200 x,y,z range (A): 69.94100 55.77300 61.38800 scale (grids/A): 0.5090004 object centre (A): -25.14550 -9.987500 26.24800 number of atom coordinates read : 3021 total number of charged atoms : 2882 net assigned charge : -0.9999670 assigned positive charge : 415.5922 centred at (gu) : 93.44666 89.49024 89.16853 assigned negative charge : -416.5934 centred at (gu) : 93.29461 89.42841 89.15054 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5212 nv = 96 ne = 84 npr = 60789 no. pairs analyzed = 60789 no. exposed pairs = 4458 no. arc points = 31780 no. surface atoms = 1489 nbur = 1532 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 220 mr = 2181 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3042 ## 395 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6528966E-11 3.6727787E-12 midg,1,midg; midg,igrid,midg -1.2249736E-10 5.6628403E-11 1,midg,midg; igrid,midg,midg -9.5462027E-11 4.8137955E-10 gauss-seidel spectral radius is 0.9801580 estimated iterations to convergence 59 setup time was (sec) 0.6500000 now iterating at: 12:23:45 rms-change max change #iterations 4.7692247E-02 8.402225 at 10iterations 4.8656617E-03 1.095142 at 20iterations 1.5549153E-03 0.3774757 at 30iterations 5.8086112E-04 0.1404305 at 40iterations 2.1704595E-04 5.2536011E-02 at 50iterations finished qdiffx linear iterations at : 12:23:49 total time elapsed so far: 5.150000 # loops : 50 mean,max change (kT/e) : 2.1704595E-04 5.2536011E-02 energy calculations done at 5.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.330000 DelPhi exited at 12:23:50 5.332u 0.469s 0:06.13 94.4% 0+0k 0+0io 6pf+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 12:23:50 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 = 3021 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.527001 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): -60.11600 9.825000 ymin,ymax (A): -37.87400 17.89900 zmin,zma (A): -4.446000 56.94200 x,y,z range (A): 69.94100 55.77300 61.38800 scale (grids/A): 1.527001 object centre (A): -25.14550 -9.987500 26.24800 number of atom coordinates read : 3021 total number of charged atoms : 2882 net assigned charge : -0.9999670 assigned positive charge : 415.5922 centred at (gu) : 100.3391 88.46968 87.50502 assigned negative charge : -416.5934 centred at (gu) : 99.88364 88.28501 87.45143 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31780 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15367 mr = 35367 m= 1418 mr = 8783 m= 29 mr = 451 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30455 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 260 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 21777 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) : 0.5090004 object centre at (A) : -25.14550 -9.987500 26.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9005485E-03 5.3001982E-03 midg,1,midg; midg,igrid,midg -3.4849918E-03 2.4924772E-03 1,midg,midg; igrid,midg,midg -3.3847461E-03 3.4481254E-03 gauss-seidel spectral radius is 0.9979365 estimated iterations to convergence 175 setup time was (sec) 0.8600000 now iterating at: 12:23:51 rms-change max change #iterations 2.724118 175.4390 at 10iterations 1.058593 47.19360 at 20iterations 0.4141129 16.73060 at 30iterations 0.1625784 6.373924 at 40iterations 6.4126536E-02 2.559192 at 50iterations 2.5867656E-02 0.9656372 at 60iterations 1.1000448E-02 0.5412827 at 70iterations 5.2886875E-03 0.2559433 at 80iterations 2.9903634E-03 0.1539001 at 90iterations 1.9592692E-03 9.4150543E-02 at 100iterations 1.3642270E-03 6.6276550E-02 at 110iterations 9.7112212E-04 4.7435760E-02 at 120iterations finished qdiffx linear iterations at : 12:24:03 total time elapsed so far: 12.04000 # loops : 120 mean,max change (kT/e) : 9.7112212E-04 4.7435760E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 12:24:03 12.211u 0.536s 0:13.02 97.8% 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 12:24:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3021 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.290502 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): -60.11600 9.825000 ymin,ymax (A): -37.87400 17.89900 zmin,zma (A): -4.446000 56.94200 x,y,z range (A): 69.94100 55.77300 61.38800 scale (grids/A): 2.290502 object centre (A): -25.14550 -9.987500 26.24800 number of atom coordinates read : 3021 total number of charged atoms : 2882 net assigned charge : -0.9999670 assigned positive charge : 415.5922 centred at (gu) : 105.5084 87.70423 86.25731 assigned negative charge : -416.5934 centred at (gu) : 104.8254 87.42731 86.17705 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 135707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31780 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 54149 mr = 88944 m= 13623 mr = 38042 m= 1834 mr = 8760 m= 73 mr = 956 m= 0 mr = 2 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 68682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 22993 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) : 1.527001 object centre at (A) : -25.14550 -9.987500 26.24800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1042745E-03 8.9136966E-02 midg,1,midg; midg,igrid,midg -6.1618440E-02 4.7655031E-02 1,midg,midg; igrid,midg,midg -3.5567198E-02 8.0456264E-02 gauss-seidel spectral radius is 0.9990626 estimated iterations to convergence 258 setup time was (sec) 1.610000 now iterating at: 12:24:05 rms-change max change #iterations 7.581794 257.6674 at 10iterations 4.256232 128.8398 at 20iterations 2.365752 74.29645 at 30iterations 1.302109 34.98621 at 40iterations 0.7123325 16.96329 at 50iterations 0.3879068 10.33047 at 60iterations 0.2110397 4.859375 at 70iterations 0.1144919 2.676660 at 80iterations 6.2029190E-02 1.721501 at 90iterations 3.3502631E-02 0.8253662 at 100iterations 1.8120158E-02 0.4245863 at 110iterations 9.8611442E-03 0.2188263 at 120iterations 5.3755939E-03 0.1221390 at 130iterations 3.0027188E-03 8.5083008E-02 at 140iterations 1.7439695E-03 4.4013977E-02 at 150iterations 1.0768613E-03 3.1179428E-02 at 160iterations 7.2018109E-04 1.9199371E-02 at 170iterations 5.1848235E-04 1.5121460E-02 at 180iterations finished qdiffx linear iterations at : 12:24:24 total time elapsed so far: 20.03000 # loops : 180 mean,max change (kT/e) : 5.1848235E-04 1.5121460E-02 energy calculations done at 20.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.20000 DelPhi exited at 12:24:24 20.202u 0.568s 0:21.02 98.7% 0+0k 0+0io 0pf+0w