Mon Oct 10 14:38:30 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 Mon Oct 10 2011 at 14:38:30 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 0.6189690 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): -23.13900 28.57500 ymin,ymax (A): -33.01400 24.50100 zmin,zma (A): -37.76700 18.26100 x,y,z range (A): 51.71400 57.51500 56.02800 scale (grids/A): 0.6189690 object centre (A): 2.718000 -4.256500 -9.752999 number of atom coordinates read : 2392 total number of charged atoms : 2237 net assigned charge : -1.999992 assigned positive charge : 354.0811 centred at (gu) : 89.76358 88.52610 89.79212 assigned negative charge : -356.0815 centred at (gu) : 89.95609 88.51897 89.75025 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6116 nv = 96 ne = 84 npr = 48646 no. pairs analyzed = 48646 no. exposed pairs = 3120 no. arc points = 21939 no. surface atoms = 1057 nbur = 1335 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3155 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7420 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2363708E-09 8.5533058E-10 midg,1,midg; midg,igrid,midg -2.7333749E-09 -8.4050894E-10 1,midg,midg; igrid,midg,midg 1.0093909E-08 -1.2504067E-08 gauss-seidel spectral radius is 0.9864689 estimated iterations to convergence 70 setup time was (sec) 0.6400000 now iterating at: 14:38:31 rms-change max change #iterations 0.1221423 19.03847 at 10iterations 1.1095259E-02 1.759152 at 20iterations 1.0322121E-03 0.1601012 at 30iterations 1.0070565E-04 1.6607285E-02 at 40iterations 1.1686176E-05 1.5201569E-03 at 50iterations finished qdiffx linear iterations at : 14:38:35 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.1686176E-05 1.5201569E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 14:38:35 4.517u 0.275s 0:05.10 93.7% 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 Mon Oct 10 2011 at 14:38:35 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 1.856907 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): -23.13900 28.57500 ymin,ymax (A): -33.01400 24.50100 zmin,zma (A): -37.76700 18.26100 x,y,z range (A): 51.71400 57.51500 56.02800 scale (grids/A): 1.856907 object centre (A): 2.718000 -4.256500 -9.752999 number of atom coordinates read : 2392 total number of charged atoms : 2237 net assigned charge : -1.999992 assigned positive charge : 354.0811 centred at (gu) : 89.29032 85.57822 89.37579 assigned negative charge : -356.0815 centred at (gu) : 89.86782 85.55678 89.25059 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 66488 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21939 grid for indexing accessible points = 1.400000 m= 22520 mr = 44916 m= 3009 mr = 15799 m= 147 mr = 1534 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 29880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17558 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) : 0.6189690 object centre at (A) : 2.718000 -4.256500 -9.752999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9437307E-02 -1.1528635E-03 midg,1,midg; midg,igrid,midg -2.1179041E-03 1.2555756E-02 1,midg,midg; igrid,midg,midg 5.5318214E-03 -3.5623409E-02 gauss-seidel spectral radius is 0.9985461 estimated iterations to convergence 208 setup time was (sec) 0.9800000 now iterating at: 14:38:36 rms-change max change #iterations 3.859512 173.3506 at 10iterations 1.756112 56.48207 at 20iterations 0.8046148 27.99712 at 30iterations 0.3656588 13.27000 at 40iterations 0.1674906 5.510044 at 50iterations 7.6513045E-02 2.704712 at 60iterations 3.5003010E-02 1.135290 at 70iterations 1.5983267E-02 0.5803976 at 80iterations 7.3294151E-03 0.2452240 at 90iterations 3.3487240E-03 0.1157913 at 100iterations 1.5467057E-03 5.2215576E-02 at 110iterations 7.1631250E-04 2.6836395E-02 at 120iterations finished qdiffx linear iterations at : 14:38:45 total time elapsed so far: 9.950000 # loops : 120 mean,max change (kT/e) : 7.1631250E-04 2.6836395E-02 energy calculations done at 9.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 14:38:46 10.145u 0.290s 0:10.89 95.7% 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 Mon Oct 10 2011 at 14:38:46 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 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: 2.785360 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): -23.13900 28.57500 ymin,ymax (A): -33.01400 24.50100 zmin,zma (A): -37.76700 18.26100 x,y,z range (A): 51.71400 57.51500 56.02800 scale (grids/A): 2.785360 object centre (A): 2.718000 -4.256500 -9.752999 number of atom coordinates read : 2392 total number of charged atoms : 2237 net assigned charge : -1.999992 assigned positive charge : 354.0811 centred at (gu) : 88.93546 83.36719 89.06350 assigned negative charge : -356.0815 centred at (gu) : 89.80168 83.33504 88.87572 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 153779 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21939 grid for indexing accessible points = 1.400000 m= 74340 mr = 109485 m= 25030 mr = 59250 m= 5005 mr = 19080 m= 582 mr = 3246 m= 28 mr = 289 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 67396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 17896 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) : 1.856907 object centre at (A) : 2.718000 -4.256500 -9.752999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3146641 -2.3940835E-02 midg,1,midg; midg,igrid,midg -5.2247480E-02 0.1969383 1,midg,midg; igrid,midg,midg 4.0594498E-03 -0.3551037 gauss-seidel spectral radius is 0.9992353 estimated iterations to convergence 285 setup time was (sec) 2.010000 now iterating at: 14:38:49 rms-change max change #iterations 9.301961 374.7290 at 10iterations 5.462446 131.7468 at 20iterations 3.162024 69.99310 at 30iterations 1.830824 44.71766 at 40iterations 1.053819 22.77913 at 50iterations 0.6064031 15.27242 at 60iterations 0.3477554 7.266986 at 70iterations 0.1991716 5.362880 at 80iterations 0.1137271 2.170635 at 90iterations 6.5078527E-02 1.337151 at 100iterations 3.7186503E-02 0.7400856 at 110iterations 2.1138888E-02 0.4550080 at 120iterations 1.2127110E-02 0.2310781 at 130iterations 6.9125509E-03 0.1516037 at 140iterations 3.9416514E-03 8.3139420E-02 at 150iterations 2.2576021E-03 4.9445152E-02 at 160iterations 1.2941363E-03 2.9366493E-02 at 170iterations 7.4905698E-04 1.4541626E-02 at 180iterations finished qdiffx linear iterations at : 14:39:03 total time elapsed so far: 16.18000 # loops : 180 mean,max change (kT/e) : 7.4905698E-04 1.4541626E-02 energy calculations done at 16.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.40000 DelPhi exited at 14:39:03 16.399u 0.336s 0:17.13 97.6% 0+0k 0+0io 0pf+0w