Tue Oct 11 05:27:52 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 Tue Oct 11 2011 at 05:27:52 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 = 2093 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: 0.7130410 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): 25.71400 72.30900 ymin,ymax (A): -19.90200 30.02500 zmin,zma (A): 3.789000 46.13300 x,y,z range (A): 46.59500 49.92700 42.34400 scale (grids/A): 0.7130410 object centre (A): 49.01150 5.061500 24.96100 number of atom coordinates read : 2093 total number of charged atoms : 1974 net assigned charge : 6.500009 assigned positive charge : 320.1639 centred at (gu) : 89.23096 90.99428 90.23505 assigned negative charge : -313.6642 centred at (gu) : 89.33038 90.93369 90.32731 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7153 nv = 96 ne = 84 npr = 42340 no. pairs analyzed = 42340 no. exposed pairs = 2558 no. arc points = 17113 no. surface atoms = 882 nbur = 1211 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 4127 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1591 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8017 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0821149E-07 9.7207984E-09 midg,1,midg; midg,igrid,midg 2.3235016E-08 1.1575059E-07 1,midg,midg; igrid,midg,midg 1.3587480E-07 5.0928168E-09 gauss-seidel spectral radius is 0.9897443 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 05:27:52 rms-change max change #iterations 0.2099933 29.34080 at 10iterations 2.6373886E-02 3.824863 at 20iterations 3.5192349E-03 0.5801277 at 30iterations 5.7574466E-04 7.7507019E-02 at 40iterations 1.5016987E-04 1.8252373E-02 at 50iterations finished qdiffx linear iterations at : 05:27:55 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.5016987E-04 1.8252373E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 05:27:56 3.322u 0.181s 0:03.83 91.3% 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 05:27:56 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 = 2093 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: 2.139123 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): 25.71400 72.30900 ymin,ymax (A): -19.90200 30.02500 zmin,zma (A): 3.789000 46.13300 x,y,z range (A): 46.59500 49.92700 42.34400 scale (grids/A): 2.139123 object centre (A): 49.01150 5.061500 24.96100 number of atom coordinates read : 2093 total number of charged atoms : 1974 net assigned charge : 6.500009 assigned positive charge : 320.1639 centred at (gu) : 87.69260 92.98307 90.70532 assigned negative charge : -313.6642 centred at (gu) : 87.99121 92.80117 90.98211 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17113 grid for indexing accessible points = 1.400000 m= 30919 mr = 54022 m= 5883 mr = 23626 m= 579 mr = 3973 m= 17 mr = 293 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 0.3900000 number of dielectric boundary points 31193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15678 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) : 0.7130410 object centre at (A) : 49.01150 5.061500 24.96100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1483274E-02 2.5666799E-02 midg,1,midg; midg,igrid,midg 3.2581054E-02 4.0167157E-02 1,midg,midg; igrid,midg,midg 4.2944655E-02 -3.5480671E-02 gauss-seidel spectral radius is 0.9988441 estimated iterations to convergence 233 setup time was (sec) 0.6100000 now iterating at: 05:27:57 rms-change max change #iterations 4.709136 211.7943 at 10iterations 2.335820 74.71542 at 20iterations 1.168222 35.62175 at 30iterations 0.5829023 18.00329 at 40iterations 0.2897826 8.806920 at 50iterations 0.1447271 4.233294 at 60iterations 7.2061390E-02 1.954836 at 70iterations 3.6026947E-02 1.026106 at 80iterations 1.8120216E-02 0.5223820 at 90iterations 9.0783443E-03 0.3007469 at 100iterations 4.6125473E-03 0.1381130 at 110iterations 2.3972117E-03 6.4783096E-02 at 120iterations finished qdiffx linear iterations at : 05:28:04 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.3972117E-03 6.4783096E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 05:28:04 7.765u 0.193s 0:08.23 96.5% 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 05:28:04 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 = 2093 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: 3.208684 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): 25.71400 72.30900 ymin,ymax (A): -19.90200 30.02500 zmin,zma (A): 3.789000 46.13300 x,y,z range (A): 46.59500 49.92700 42.34400 scale (grids/A): 3.208684 object centre (A): 49.01150 5.061500 24.96100 number of atom coordinates read : 2093 total number of charged atoms : 1974 net assigned charge : 6.500009 assigned positive charge : 320.1639 centred at (gu) : 86.53887 94.47449 91.05802 assigned negative charge : -313.6642 centred at (gu) : 86.98692 94.20174 91.47314 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 174516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17113 grid for indexing accessible points = 1.400000 m= 96174 mr = 129932 m= 39193 mr = 80410 m= 11109 mr = 32343 m= 2253 mr = 8645 m= 274 mr = 1648 m= 12 mr = 181 m= 0 mr = 3 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 70369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 15792 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) : 2.139123 object centre at (A) : 49.01150 5.061500 24.96100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2091846 0.2168651 midg,1,midg; midg,igrid,midg 0.2423946 0.2932723 1,midg,midg; igrid,midg,midg 0.4057030 -0.3921804 gauss-seidel spectral radius is 0.9992999 estimated iterations to convergence 298 setup time was (sec) 1.420000 now iterating at: 05:28:06 rms-change max change #iterations 10.44615 342.7102 at 10iterations 6.194584 183.6014 at 20iterations 3.685193 85.27091 at 30iterations 2.181719 42.87174 at 40iterations 1.289283 24.27882 at 50iterations 0.7591472 15.11612 at 60iterations 0.4476815 9.930717 at 70iterations 0.2631089 5.011805 at 80iterations 0.1546718 2.778742 at 90iterations 9.1089502E-02 1.587962 at 100iterations 5.3608350E-02 0.9216003 at 110iterations 3.1604864E-02 0.5836201 at 120iterations 1.8697275E-02 0.3416910 at 130iterations 1.1211162E-02 0.1999512 at 140iterations 6.8613756E-03 0.1270714 at 150iterations 4.3360726E-03 7.6561332E-02 at 160iterations 2.8874767E-03 5.0819397E-02 at 170iterations 2.0457241E-03 3.5827637E-02 at 180iterations finished qdiffx linear iterations at : 05:28:17 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 2.0457241E-03 3.5827637E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 05:28:18 12.750u 0.199s 0:13.45 96.2% 0+0k 0+0io 0pf+0w