Sat Oct 15 11:52:25 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 15 2011 at 11:52:25 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 = 2244 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6573602 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): -29.85800 22.25400 ymin,ymax (A): 27.50000 71.23700 zmin,zma (A): -13.20200 40.95400 x,y,z range (A): 52.11200 43.73700 54.15600 scale (grids/A): 0.6573602 object centre (A): -3.802000 49.36850 13.87600 number of atom coordinates read : 2244 total number of charged atoms : 2110 net assigned charge : 12.50002 assigned positive charge : 326.4616 centred at (gu) : 91.52351 91.44345 89.44909 assigned negative charge : -313.9622 centred at (gu) : 91.47824 91.37999 89.44120 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 44836 no. pairs analyzed = 44836 no. exposed pairs = 3031 no. arc points = 21571 no. surface atoms = 1018 nbur = 1226 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 3489 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2080 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1287762E-08 2.7170616E-08 midg,1,midg; midg,igrid,midg 1.4867036E-08 5.1907602E-08 1,midg,midg; igrid,midg,midg 1.6626196E-08 4.9062944E-08 gauss-seidel spectral radius is 0.9879850 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 11:52:25 rms-change max change #iterations 0.1480386 25.01815 at 10iterations 1.5478141E-02 2.528124 at 20iterations 1.7029337E-03 0.2355328 at 30iterations 2.1309353E-04 3.6594391E-02 at 40iterations 3.4351047E-05 6.1492920E-03 at 50iterations finished qdiffx linear iterations at : 11:52:28 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.4351047E-05 6.1492920E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 11:52:29 3.425u 0.177s 0:03.90 92.0% 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 Sat Oct 15 2011 at 11:52:29 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 = 2244 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.972081 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): -29.85800 22.25400 ymin,ymax (A): 27.50000 71.23700 zmin,zma (A): -13.20200 40.95400 x,y,z range (A): 52.11200 43.73700 54.15600 scale (grids/A): 1.972081 object centre (A): -3.802000 49.36850 13.87600 number of atom coordinates read : 2244 total number of charged atoms : 2110 net assigned charge : 12.50002 assigned positive charge : 326.4616 centred at (gu) : 94.57018 94.33027 88.34707 assigned negative charge : -313.9622 centred at (gu) : 94.43483 94.14001 88.32361 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21571 grid for indexing accessible points = 1.400000 m= 26946 mr = 47575 m= 4975 mr = 19396 m= 409 mr = 3089 m= 8 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 157 time to turn everything in is 0.3600000 number of dielectric boundary points 33673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 16648 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) : 0.6573602 object centre at (A) : -3.802000 49.36850 13.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8028977E-02 4.9142189E-02 midg,1,midg; midg,igrid,midg 4.1740080E-03 3.4971617E-02 1,midg,midg; igrid,midg,midg 5.5825464E-02 3.6215555E-02 gauss-seidel spectral radius is 0.9986988 estimated iterations to convergence 220 setup time was (sec) 0.5700000 now iterating at: 11:52:30 rms-change max change #iterations 4.014588 195.0133 at 10iterations 1.909561 80.34799 at 20iterations 0.9071140 33.06219 at 30iterations 0.4318000 13.82900 at 40iterations 0.2054811 7.564049 at 50iterations 9.8015375E-02 3.131817 at 60iterations 4.6552066E-02 1.555372 at 70iterations 2.2213586E-02 0.7426551 at 80iterations 1.0608785E-02 0.3624229 at 90iterations 5.0768703E-03 0.1658649 at 100iterations 2.4254518E-03 7.3468685E-02 at 110iterations 1.1675174E-03 4.1392326E-02 at 120iterations finished qdiffx linear iterations at : 11:52:37 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.1675174E-03 4.1392326E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 11:52:37 7.936u 0.227s 0:08.43 96.6% 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 15 2011 at 11:52:37 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 = 2244 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.958121 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): -29.85800 22.25400 ymin,ymax (A): 27.50000 71.23700 zmin,zma (A): -13.20200 40.95400 x,y,z range (A): 52.11200 43.73700 54.15600 scale (grids/A): 2.958121 object centre (A): -3.802000 49.36850 13.87600 number of atom coordinates read : 2244 total number of charged atoms : 2110 net assigned charge : 12.50002 assigned positive charge : 326.4616 centred at (gu) : 96.85525 96.49537 87.52054 assigned negative charge : -313.9622 centred at (gu) : 96.65230 96.21007 87.48540 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 164549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21571 grid for indexing accessible points = 1.400000 m= 84320 mr = 115340 m= 33243 mr = 67581 m= 9167 mr = 26437 m= 1616 mr = 6746 m= 131 mr = 1072 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 528 time to turn everything in is 0.9400000 number of dielectric boundary points 75786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 16876 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) : 1.972081 object centre at (A) : -3.802000 49.36850 13.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4728273 0.4962527 midg,1,midg; midg,igrid,midg 3.1705167E-02 0.2988546 1,midg,midg; igrid,midg,midg 0.8583815 0.3405650 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.180000 now iterating at: 11:52:39 rms-change max change #iterations 9.649128 399.7775 at 10iterations 5.727369 140.2858 at 20iterations 3.395851 83.19650 at 30iterations 2.002994 48.00438 at 40iterations 1.174295 26.80722 at 50iterations 0.6875829 14.11263 at 60iterations 0.4027864 9.151126 at 70iterations 0.2341443 4.706126 at 80iterations 0.1371104 2.777929 at 90iterations 7.9742417E-02 1.653150 at 100iterations 4.6356056E-02 0.9157104 at 110iterations 2.7000640E-02 0.5136642 at 120iterations 1.5694685E-02 0.3067989 at 130iterations 9.1200871E-03 0.1848946 at 140iterations 5.3001540E-03 9.7923279E-02 at 150iterations 3.0799885E-03 5.6571960E-02 at 160iterations 1.7907767E-03 3.7572384E-02 at 170iterations 1.0439862E-03 1.8257141E-02 at 180iterations finished qdiffx linear iterations at : 11:52:50 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.0439862E-03 1.8257141E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 11:52:51 12.846u 0.220s 0:13.37 97.6% 0+0k 0+0io 0pf+0w