Sun Oct 9 19:30:49 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 19:30:49 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5531 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5028178 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): 3.140000 68.16600 ymin,ymax (A): -9.029000 53.44300 zmin,zma (A): -2.056000 68.74500 x,y,z range (A): 65.02600 62.47200 70.80099 scale (grids/A): 0.5028178 object centre (A): 35.65300 22.20700 33.34450 number of atom coordinates read : 5531 total number of charged atoms : 5353 net assigned charge : 4.740028 assigned positive charge : 844.0147 centred at (gu) : 88.44376 89.33143 88.91929 assigned negative charge : -839.2810 centred at (gu) : 88.38412 89.36643 88.85508 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8933 nv = 96 ne = 84 npr = 112391 no. pairs analyzed = 112391 no. exposed pairs = 6417 no. arc points = 43658 no. surface atoms = 2177 nbur = 3354 mkacc time = 0.1900000 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 = 1.708000 m= 297 mr = 4949 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4377 ## 641 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2122967E-10 1.4103742E-10 midg,1,midg; midg,igrid,midg 1.5052835E-10 -2.1056505E-11 1,midg,midg; igrid,midg,midg -1.2323714E-10 1.1798998E-10 gauss-seidel spectral radius is 0.9798225 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 19:30:50 rms-change max change #iterations 7.3876567E-02 10.50841 at 10iterations 1.0674340E-02 1.655849 at 20iterations 4.6585202E-03 0.7757111 at 30iterations 2.2082049E-03 0.3628464 at 40iterations 1.0604338E-03 0.1694107 at 50iterations finished qdiffx linear iterations at : 19:30:53 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.0604338E-03 0.1694107 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 19:30:54 3.655u 0.155s 0:04.08 93.1% 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 Sun Oct 9 2011 at 19:30:54 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5531 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.508453 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): 3.140000 68.16600 ymin,ymax (A): -9.029000 53.44300 zmin,zma (A): -2.056000 68.74500 x,y,z range (A): 65.02600 62.47200 70.80099 scale (grids/A): 1.508453 object centre (A): 35.65300 22.20700 33.34450 number of atom coordinates read : 5531 total number of charged atoms : 5353 net assigned charge : 4.740028 assigned positive charge : 844.0147 centred at (gu) : 85.32951 87.99262 86.75615 assigned negative charge : -839.2810 centred at (gu) : 85.15213 88.09888 86.56503 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 102510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43658 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 31295 mr = 73974 m= 2694 mr = 21567 m= 47 mr = 1137 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 39868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 616 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 40029 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) : 0.5028178 object centre at (A) : 35.65300 22.20700 33.34450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2632651E-02 1.5552466E-02 midg,1,midg; midg,igrid,midg 1.1995064E-02 4.4943388E-03 1,midg,midg; igrid,midg,midg -8.8588241E-03 1.4214038E-03 gauss-seidel spectral radius is 0.9981011 estimated iterations to convergence 182 setup time was (sec) 0.7100000 now iterating at: 19:30:54 rms-change max change #iterations 4.051194 171.2483 at 10iterations 1.658773 52.92542 at 20iterations 0.6781924 23.25867 at 30iterations 0.2785139 8.439178 at 40iterations 0.1157959 3.885551 at 50iterations 4.9220540E-02 1.477486 at 60iterations 2.2412734E-02 0.7704697 at 70iterations 1.1698777E-02 0.3929977 at 80iterations 7.3382878E-03 0.2612839 at 90iterations 5.1183049E-03 0.1789551 at 100iterations 3.7732881E-03 0.1244965 at 110iterations 2.8330036E-03 9.0393066E-02 at 120iterations finished qdiffx linear iterations at : 19:31:02 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 2.8330036E-03 9.0393066E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 19:31:02 8.093u 0.206s 0:08.62 96.1% 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 Sun Oct 9 2011 at 19:31:02 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5531 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.262680 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): 3.140000 68.16600 ymin,ymax (A): -9.029000 53.44300 zmin,zma (A): -2.056000 68.74500 x,y,z range (A): 65.02600 62.47200 70.80099 scale (grids/A): 2.262680 object centre (A): 35.65300 22.20700 33.34450 number of atom coordinates read : 5531 total number of charged atoms : 5353 net assigned charge : 4.740028 assigned positive charge : 844.0147 centred at (gu) : 82.99402 86.98845 85.13370 assigned negative charge : -839.2810 centred at (gu) : 82.72827 87.14835 84.84764 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 238934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43658 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 112254 mr = 180735 m= 28842 mr = 89655 m= 3777 mr = 21283 m= 196 mr = 2295 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.210000 number of dielectric boundary points 89965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 42659 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) : 1.508453 object centre at (A) : 35.65300 22.20700 33.34450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3294159 0.5979195 midg,1,midg; midg,igrid,midg 0.2154902 4.1613623E-02 1,midg,midg; igrid,midg,midg -0.2491557 -4.3842490E-03 gauss-seidel spectral radius is 0.9991602 estimated iterations to convergence 273 setup time was (sec) 1.450000 now iterating at: 19:31:04 rms-change max change #iterations 10.86104 280.8685 at 10iterations 6.194199 147.0321 at 20iterations 3.497992 71.88600 at 30iterations 1.970578 38.28836 at 40iterations 1.105906 22.12154 at 50iterations 0.6178738 11.99044 at 60iterations 0.3451470 6.813553 at 70iterations 0.1928920 3.195919 at 80iterations 0.1078869 2.118835 at 90iterations 6.0515296E-02 1.165405 at 100iterations 3.4310073E-02 0.6379509 at 110iterations 1.9831220E-02 0.3648796 at 120iterations 1.1936821E-02 0.2452087 at 130iterations 7.6476275E-03 0.1545646 at 140iterations 5.2729631E-03 0.1069450 at 150iterations 3.9197570E-03 8.0741882E-02 at 160iterations 3.0706003E-03 6.0043335E-02 at 170iterations 2.4773579E-03 4.6379089E-02 at 180iterations finished qdiffx linear iterations at : 19:31:16 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 2.4773579E-03 4.6379089E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 19:31:16 13.297u 0.222s 0:13.78 98.0% 0+0k 0+0io 0pf+0w