Tue Nov 22 14:17:14 PST 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 Nov 22 2011 at 14:17:18 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 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: 0.6539310 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): -5.126000 34.81500 ymin,ymax (A): -3.454000 49.30800 zmin,zma (A): -7.892000 46.54800 x,y,z range (A): 39.94100 52.76200 54.44000 scale (grids/A): 0.6539310 object centre (A): 14.84450 22.92700 19.32800 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000010 assigned positive charge : 292.5599 centred at (gu) : 89.37564 92.19138 90.09349 assigned negative charge : -287.5602 centred at (gu) : 89.30363 92.29723 90.14008 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5793 nv = 96 ne = 84 npr = 39710 no. pairs analyzed = 39710 no. exposed pairs = 2582 no. arc points = 18245 no. surface atoms = 876 nbur = 1080 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3129 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1867 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6735 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6568830E-08 5.3820699E-09 midg,1,midg; midg,igrid,midg 1.5376209E-08 -4.0210386E-09 1,midg,midg; igrid,midg,midg 2.2891109E-09 1.7590224E-08 gauss-seidel spectral radius is 0.9878277 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 14:17:21 rms-change max change #iterations 0.1419527 23.66199 at 10iterations 1.4289616E-02 2.361728 at 20iterations 1.4868412E-03 0.2584023 at 30iterations 1.5492053E-04 2.6326656E-02 at 40iterations 1.5804437E-05 2.4909973E-03 at 50iterations finished qdiffx linear iterations at : 14:17:32 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 1.5804437E-05 2.4909973E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 14:17:33 3.938u 0.246s 0:15.90 26.2% 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 Nov 22 2011 at 14:17:35 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 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: 1.961793 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): -5.126000 34.81500 ymin,ymax (A): -3.454000 49.30800 zmin,zma (A): -7.892000 46.54800 x,y,z range (A): 39.94100 52.76200 54.44000 scale (grids/A): 1.961793 object centre (A): 14.84450 22.92700 19.32800 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000010 assigned positive charge : 292.5599 centred at (gu) : 88.12698 96.57437 90.28040 assigned negative charge : -287.5602 centred at (gu) : 87.91115 96.89191 90.42048 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18245 grid for indexing accessible points = 1.400000 m= 22747 mr = 42058 m= 3438 mr = 17113 m= 194 mr = 2181 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 450 time to turn everything in is 0.3300000 number of dielectric boundary points 27024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14405 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) : 0.6539310 object centre at (A) : 14.84450 22.92700 19.32800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8424917E-03 3.3446644E-02 midg,1,midg; midg,igrid,midg 4.1977677E-02 1.8265195E-03 1,midg,midg; igrid,midg,midg 7.6287938E-03 1.2463436E-02 gauss-seidel spectral radius is 0.9986394 estimated iterations to convergence 215 setup time was (sec) 0.5700000 now iterating at: 14:17:40 rms-change max change #iterations 3.828780 162.9375 at 10iterations 1.796012 70.83243 at 20iterations 0.8379724 30.08963 at 30iterations 0.3937609 14.30387 at 40iterations 0.1841483 6.737768 at 50iterations 8.6100496E-02 2.868855 at 60iterations 4.0363971E-02 1.303397 at 70iterations 1.8925084E-02 0.6744232 at 80iterations 8.8545289E-03 0.2876962 at 90iterations 4.1425340E-03 0.1516180 at 100iterations 1.9339751E-03 6.5937042E-02 at 110iterations 9.0851920E-04 3.2645464E-02 at 120iterations finished qdiffx linear iterations at : 14:18:05 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 9.0851920E-04 3.2645464E-02 energy calculations done at 8.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.960000 DelPhi exited at 14:18:07 8.959u 0.267s 0:31.59 29.1% 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 Tue Nov 22 2011 at 14:18:09 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 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: 2.942689 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): -5.126000 34.81500 ymin,ymax (A): -3.454000 49.30800 zmin,zma (A): -7.892000 46.54800 x,y,z range (A): 39.94100 52.76200 54.44000 scale (grids/A): 2.942689 object centre (A): 14.84450 22.92700 19.32800 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000010 assigned positive charge : 292.5599 centred at (gu) : 87.19049 99.86150 90.42055 assigned negative charge : -287.5602 centred at (gu) : 86.86684 100.3379 90.63081 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 143094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18245 grid for indexing accessible points = 1.400000 m= 73001 mr = 101895 m= 27058 mr = 60095 m= 6286 mr = 22115 m= 842 mr = 4766 m= 41 mr = 533 m= 0 mr = 18 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1533 time to turn everything in is 0.8600000 number of dielectric boundary points 60900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14592 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) : 1.961793 object centre at (A) : 14.84450 22.92700 19.32800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4045235E-02 0.7732193 midg,1,midg; midg,igrid,midg 0.4466681 -4.6901807E-02 1,midg,midg; igrid,midg,midg 0.1157702 9.3841158E-02 gauss-seidel spectral radius is 0.9992523 estimated iterations to convergence 289 setup time was (sec) 1.140000 now iterating at: 14:18:16 rms-change max change #iterations 9.079893 383.5449 at 10iterations 5.302199 152.3776 at 20iterations 3.073649 103.3807 at 30iterations 1.777643 41.63028 at 40iterations 1.024883 21.43075 at 50iterations 0.5888903 14.13175 at 60iterations 0.3384467 7.552231 at 70iterations 0.1941200 3.836635 at 80iterations 0.1113523 2.228456 at 90iterations 6.3808240E-02 1.286520 at 100iterations 3.6597617E-02 0.7457581 at 110iterations 2.0940818E-02 0.3962059 at 120iterations 1.1997877E-02 0.2186704 at 130iterations 6.8595959E-03 0.1336122 at 140iterations 3.9277766E-03 8.0235958E-02 at 150iterations 2.2449228E-03 4.4251084E-02 at 160iterations 1.2814309E-03 2.8156281E-02 at 170iterations 7.3570979E-04 1.5047073E-02 at 180iterations finished qdiffx linear iterations at : 14:18:55 total time elapsed so far: 14.06000 # loops : 180 mean,max change (kT/e) : 7.3570979E-04 1.5047073E-02 energy calculations done at 14.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.20000 DelPhi exited at 14:18:56 14.198u 0.282s 0:47.30 30.5% 0+0k 0+0io 0pf+0w