Sat Oct 15 10:23:30 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+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 10:23:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4468 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5909008 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): -24.86600 34.95700 ymin,ymax (A): 34.79300 95.04000 zmin,zma (A): 30.38600 89.43100 x,y,z range (A): 59.82300 60.24700 59.04500 scale (grids/A): 0.5909008 object centre (A): 5.045499 64.91650 59.90850 number of atom coordinates read : 4468 total number of charged atoms : 4309 net assigned charge : -1.999937 assigned positive charge : 672.1539 centred at (gu) : 90.48904 89.22941 88.83940 assigned negative charge : -674.1572 centred at (gu) : 90.35738 89.38966 88.99531 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9934 nv = 96 ne = 84 npr = 94754 no. pairs analyzed = 94754 no. exposed pairs = 5000 no. arc points = 34004 no. surface atoms = 1703 nbur = 2765 mkacc time = 0.2700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 492 mr = 5820 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 170 time to turn everything in is 0.5300000 number of dielectric boundary points 4540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3672 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 13099 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5163920E-09 -6.3888610E-09 midg,1,midg; midg,igrid,midg 7.9993221E-09 -7.1706849E-09 1,midg,midg; igrid,midg,midg -6.3997549E-09 6.0085861E-09 gauss-seidel spectral radius is 0.9853207 estimated iterations to convergence 68 setup time was (sec) 0.8200000 now iterating at: 10:23:32 rms-change max change #iterations 0.1321528 18.50668 at 10iterations 1.1451043E-02 1.430798 at 20iterations 1.2311938E-03 0.1636887 at 30iterations 2.6506613E-04 3.0895233E-02 at 40iterations 8.7141743E-05 9.9477470E-03 at 50iterations finished qdiffx linear iterations at : 10:23:35 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 8.7141743E-05 9.9477470E-03 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 10:23:35 4.429u 0.274s 0:05.02 93.4% 0+0k 0+0io 6pf+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 10:23:36 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 = 4468 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.772702 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): -24.86600 34.95700 ymin,ymax (A): 34.79300 95.04000 zmin,zma (A): 30.38600 89.43100 x,y,z range (A): 59.82300 60.24700 59.04500 scale (grids/A): 1.772702 object centre (A): 5.045499 64.91650 59.90850 number of atom coordinates read : 4468 total number of charged atoms : 4309 net assigned charge : -1.999937 assigned positive charge : 672.1539 centred at (gu) : 91.46595 87.68690 86.51687 assigned negative charge : -674.1572 centred at (gu) : 91.07174 88.16843 86.98562 start vw surface at 0.1900000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 110644 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34004 grid for indexing accessible points = 1.400000 m= 38554 mr = 80592 m= 5354 mr = 28705 m= 249 mr = 3431 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 8586 time to turn everything in is 0.9300000 number of dielectric boundary points 42001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 346 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 33531 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) : 0.5909008 object centre at (A) : 5.045499 64.91650 59.90850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7108876E-02 -3.8986880E-02 midg,1,midg; midg,igrid,midg 3.6933742E-02 -2.2329943E-02 1,midg,midg; igrid,midg,midg -7.3231882E-03 3.8583592E-02 gauss-seidel spectral radius is 0.9985901 estimated iterations to convergence 211 setup time was (sec) 1.220000 now iterating at: 10:23:37 rms-change max change #iterations 5.062510 198.3503 at 10iterations 2.334755 67.79578 at 20iterations 1.079828 28.40290 at 30iterations 0.5003525 15.16654 at 40iterations 0.2315864 6.234756 at 50iterations 0.1075506 2.775775 at 60iterations 4.9890131E-02 1.362654 at 70iterations 2.3205217E-02 0.6330814 at 80iterations 1.0782803E-02 0.2960587 at 90iterations 5.0165872E-03 0.1302071 at 100iterations 2.3600254E-03 6.2776566E-02 at 110iterations 1.1229855E-03 2.8946698E-02 at 120iterations finished qdiffx linear iterations at : 10:23:46 total time elapsed so far: 10.13000 # loops : 120 mean,max change (kT/e) : 1.1229855E-03 2.8946698E-02 energy calculations done at 10.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.31000 DelPhi exited at 10:23:47 10.308u 0.382s 0:11.29 94.5% 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 Sat Oct 15 2011 at 10:23:47 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 = 4468 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.659054 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): -24.86600 34.95700 ymin,ymax (A): 34.79300 95.04000 zmin,zma (A): 30.38600 89.43100 x,y,z range (A): 59.82300 60.24700 59.04500 scale (grids/A): 2.659054 object centre (A): 5.045499 64.91650 59.90850 number of atom coordinates read : 4468 total number of charged atoms : 4309 net assigned charge : -1.999937 assigned positive charge : 672.1539 centred at (gu) : 92.19854 86.53008 84.77489 assigned negative charge : -674.1572 centred at (gu) : 91.60744 87.25240 85.47820 start vw surface at 0.2100000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 257103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34004 grid for indexing accessible points = 1.400000 m= 129244 mr = 195569 m= 42803 mr = 107138 m= 9271 mr = 34448 m= 1085 mr = 7016 m= 53 mr = 732 m= 0 mr = 26 time to grow re-entrant surface = 1.490000 no. cavity mid-points inaccessible to solvent = 29106 time to turn everything in is 2.470000 number of dielectric boundary points 94630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.640000 number of grid points assigned charge 34457 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) : 1.772702 object centre at (A) : 5.045499 64.91650 59.90850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4140312 -0.4460406 midg,1,midg; midg,igrid,midg 0.4145102 -0.4479750 1,midg,midg; igrid,midg,midg 1.2516038E-02 0.3126869 gauss-seidel spectral radius is 0.9992750 estimated iterations to convergence 293 setup time was (sec) 2.830000 now iterating at: 10:23:50 rms-change max change #iterations 12.17203 269.3502 at 10iterations 7.218561 146.9575 at 20iterations 4.231220 89.14591 at 30iterations 2.475962 44.91061 at 40iterations 1.450116 24.05830 at 50iterations 0.8436491 14.08678 at 60iterations 0.4912252 8.225834 at 70iterations 0.2852235 4.778664 at 80iterations 0.1655633 2.582451 at 90iterations 9.6150704E-02 1.507817 at 100iterations 5.5805720E-02 0.8855060 at 110iterations 3.2363709E-02 0.5225830 at 120iterations 1.8794486E-02 0.2834277 at 130iterations 1.0921152E-02 0.1859660 at 140iterations 6.3760611E-03 9.9152565E-02 at 150iterations 3.7335372E-03 6.7520618E-02 at 160iterations 2.2225627E-03 3.4820557E-02 at 170iterations 1.3445873E-03 2.1558762E-02 at 180iterations finished qdiffx linear iterations at : 10:24:05 total time elapsed so far: 18.05000 # loops : 180 mean,max change (kT/e) : 1.3445873E-03 2.1558762E-02 energy calculations done at 18.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.24000 DelPhi exited at 10:24:06 18.239u 0.342s 0:19.18 96.8% 0+0k 0+0io 0pf+0w