Tue Oct 11 06:40:02 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 Tue Oct 11 2011 at 06:40:02 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7012014 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): -20.24600 23.63300 ymin,ymax (A): -26.72000 10.68900 zmin,zma (A): -14.11500 36.65500 x,y,z range (A): 43.87900 37.40900 50.77000 scale (grids/A): 0.7012014 object centre (A): 1.693501 -8.015501 11.27000 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.0191 centred at (gu) : 90.09453 90.89242 89.31968 assigned negative charge : -307.0741 centred at (gu) : 89.90636 90.87569 89.29246 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6835 nv = 96 ne = 84 npr = 41728 no. pairs analyzed = 41728 no. exposed pairs = 2447 no. arc points = 16961 no. surface atoms = 834 nbur = 1231 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 3959 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1599 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7675 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4202917E-08 5.4395567E-08 midg,1,midg; midg,igrid,midg 3.6731048E-08 6.8272662E-08 1,midg,midg; igrid,midg,midg -2.9940875E-08 1.3090479E-07 gauss-seidel spectral radius is 0.9893979 estimated iterations to convergence 79 setup time was (sec) 0.4700000 now iterating at: 06:40:02 rms-change max change #iterations 0.1904000 35.32221 at 10iterations 2.3786552E-02 3.272779 at 20iterations 3.0674431E-03 0.4360676 at 30iterations 4.8643941E-04 6.7802429E-02 at 40iterations 1.1411456E-04 1.7087936E-02 at 50iterations finished qdiffx linear iterations at : 06:40:05 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.1411456E-04 1.7087936E-02 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 06:40:06 3.109u 0.145s 0:03.78 85.7% 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 Tue Oct 11 2011 at 06:40:06 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.103604 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): -20.24600 23.63300 ymin,ymax (A): -26.72000 10.68900 zmin,zma (A): -14.11500 36.65500 x,y,z range (A): 43.87900 37.40900 50.77000 scale (grids/A): 2.103604 object centre (A): 1.693501 -8.015501 11.27000 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.0191 centred at (gu) : 90.28363 92.67719 87.95892 assigned negative charge : -307.0741 centred at (gu) : 89.71918 92.62704 87.87739 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16961 grid for indexing accessible points = 1.400000 m= 28988 mr = 52254 m= 5487 mr = 21915 m= 492 mr = 3650 m= 8 mr = 244 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 0.5300000 number of dielectric boundary points 30107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15335 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) : 0.7012014 object centre at (A) : 1.693501 -8.015501 11.27000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2779285E-02 4.3990608E-02 midg,1,midg; midg,igrid,midg 6.5101795E-03 3.1033020E-02 1,midg,midg; igrid,midg,midg -1.9603504E-03 4.1444410E-02 gauss-seidel spectral radius is 0.9988112 estimated iterations to convergence 230 setup time was (sec) 0.8000000 now iterating at: 06:40:07 rms-change max change #iterations 4.471552 204.4670 at 10iterations 2.194297 75.06887 at 20iterations 1.080449 33.70334 at 30iterations 0.5354932 18.00121 at 40iterations 0.2642592 7.854416 at 50iterations 0.1311949 3.983670 at 60iterations 6.4435080E-02 2.011038 at 70iterations 3.1964928E-02 1.066765 at 80iterations 1.5842583E-02 0.4928818 at 90iterations 7.8777801E-03 0.2324448 at 100iterations 3.9453804E-03 0.1208420 at 110iterations 1.9941051E-03 6.6314697E-02 at 120iterations finished qdiffx linear iterations at : 06:40:13 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 1.9941051E-03 6.6314697E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 06:40:13 7.063u 0.217s 0:07.57 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 Tue Oct 11 2011 at 06:40:13 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.155406 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): -20.24600 23.63300 ymin,ymax (A): -26.72000 10.68900 zmin,zma (A): -14.11500 36.65500 x,y,z range (A): 43.87900 37.40900 50.77000 scale (grids/A): 3.155406 object centre (A): 1.693501 -8.015501 11.27000 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.0191 centred at (gu) : 90.42541 94.01577 86.93845 assigned negative charge : -307.0741 centred at (gu) : 89.57869 93.94058 86.81609 start vw surface at 0.1400000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 169033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16961 grid for indexing accessible points = 1.400000 m= 91020 mr = 125838 m= 36410 mr = 75972 m= 10525 mr = 29853 m= 2099 mr = 8114 m= 200 mr = 1519 m= 7 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 67873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 15448 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) : 2.103604 object centre at (A) : 1.693501 -8.015501 11.27000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5830646 0.3660222 midg,1,midg; midg,igrid,midg 3.5087168E-02 0.2523832 1,midg,midg; igrid,midg,midg 6.7926288E-02 0.3372638 gauss-seidel spectral radius is 0.9992886 estimated iterations to convergence 296 setup time was (sec) 1.910000 now iterating at: 06:40:15 rms-change max change #iterations 10.12023 341.6505 at 10iterations 5.968299 175.1377 at 20iterations 3.521838 74.20462 at 30iterations 2.072939 47.52508 at 40iterations 1.219199 23.30019 at 50iterations 0.7146533 13.29520 at 60iterations 0.4187022 8.588058 at 70iterations 0.2443508 4.485840 at 80iterations 0.1432073 2.745451 at 90iterations 8.3759509E-02 1.589256 at 100iterations 4.9056411E-02 1.043536 at 110iterations 2.8757658E-02 0.5033112 at 120iterations 1.7011357E-02 0.2981987 at 130iterations 1.0142900E-02 0.2012177 at 140iterations 6.1697573E-03 0.1174316 at 150iterations 3.8588620E-03 7.1212769E-02 at 160iterations 2.5153828E-03 4.7172546E-02 at 170iterations 1.7293894E-03 3.1925201E-02 at 180iterations finished qdiffx linear iterations at : 06:40:25 total time elapsed so far: 11.51000 # loops : 180 mean,max change (kT/e) : 1.7293894E-03 3.1925201E-02 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 06:40:26 11.695u 0.161s 0:12.30 96.3% 0+0k 0+0io 0pf+0w