Mon Oct 10 09:45:09 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 Mon Oct 10 2011 at 09:45:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2816 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: 0.5805137 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): -17.76100 36.15500 ymin,ymax (A): -64.96300 -4.545000 zmin,zma (A): -3.339000 57.98600 x,y,z range (A): 53.91600 60.41800 61.32500 scale (grids/A): 0.5805137 object centre (A): 9.197000 -34.75400 27.32350 number of atom coordinates read : 2816 total number of charged atoms : 2667 net assigned charge : 7.000018 assigned positive charge : 412.6870 centred at (gu) : 89.26611 89.45306 87.60862 assigned negative charge : -405.6873 centred at (gu) : 89.40945 89.32395 87.45358 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6549 nv = 96 ne = 84 npr = 53841 no. pairs analyzed = 53841 no. exposed pairs = 4143 no. arc points = 30579 no. surface atoms = 1373 nbur = 1443 mkacc time = 0.1500000 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 = 1.512000 m= 307 mr = 2922 m= 0 mr = 12 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3097 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8169 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8826688E-09 2.7133769E-09 midg,1,midg; midg,igrid,midg -1.1824342E-09 3.7014372E-09 1,midg,midg; igrid,midg,midg 5.3278497E-09 -1.1019978E-09 gauss-seidel spectral radius is 0.9846909 estimated iterations to convergence 66 setup time was (sec) 0.6300000 now iterating at: 09:45:10 rms-change max change #iterations 9.4014376E-02 16.89766 at 10iterations 7.0761116E-03 1.132679 at 20iterations 5.7206384E-04 8.4220886E-02 at 30iterations 4.8034119E-05 8.1825256E-03 at 40iterations 5.5279174E-06 7.3432922E-04 at 50iterations finished qdiffx linear iterations at : 09:45:14 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 5.5279174E-06 7.3432922E-04 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 09:45:15 4.536u 0.397s 0:05.33 92.3% 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 Mon Oct 10 2011 at 09:45:15 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 = 2816 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: 1.741541 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): -17.76100 36.15500 ymin,ymax (A): -64.96300 -4.545000 zmin,zma (A): -3.339000 57.98600 x,y,z range (A): 53.91600 60.41800 61.32500 scale (grids/A): 1.741541 object centre (A): 9.197000 -34.75400 27.32350 number of atom coordinates read : 2816 total number of charged atoms : 2667 net assigned charge : 7.000018 assigned positive charge : 412.6870 centred at (gu) : 87.79794 88.35851 82.82592 assigned negative charge : -405.6873 centred at (gu) : 88.22802 87.97158 82.36028 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30579 grid for indexing accessible points = 1.400000 m= 21892 mr = 42718 m= 2874 mr = 14024 m= 122 mr = 1345 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 151 time to turn everything in is 0.6000000 number of dielectric boundary points 36309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20762 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) : 0.5805137 object centre at (A) : 9.197000 -34.75400 27.32350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7132614E-03 1.6175531E-02 midg,1,midg; midg,igrid,midg 2.6166357E-02 3.8839135E-02 1,midg,midg; igrid,midg,midg 1.6306117E-02 1.8212434E-03 gauss-seidel spectral radius is 0.9984189 estimated iterations to convergence 200 setup time was (sec) 0.9000000 now iterating at: 09:45:16 rms-change max change #iterations 3.662663 156.7148 at 10iterations 1.612427 74.61927 at 20iterations 0.7086685 24.64638 at 30iterations 0.3108975 11.63869 at 40iterations 0.1365818 4.544863 at 50iterations 6.0389310E-02 2.117325 at 60iterations 2.6613647E-02 0.9086785 at 70iterations 1.1766749E-02 0.4295502 at 80iterations 5.1606637E-03 0.1956310 at 90iterations 2.2786281E-03 8.1486702E-02 at 100iterations 1.0018866E-03 3.6010742E-02 at 110iterations 4.4251731E-04 1.4701843E-02 at 120iterations finished qdiffx linear iterations at : 09:45:26 total time elapsed so far: 10.60000 # loops : 120 mean,max change (kT/e) : 4.4251731E-04 1.4701843E-02 energy calculations done at 10.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.76000 DelPhi exited at 09:45:26 10.762u 0.457s 0:11.60 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 Mon Oct 10 2011 at 09:45:26 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 = 2816 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: 2.612311 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): -17.76100 36.15500 ymin,ymax (A): -64.96300 -4.545000 zmin,zma (A): -3.339000 57.98600 x,y,z range (A): 53.91600 60.41800 61.32500 scale (grids/A): 2.612311 object centre (A): 9.197000 -34.75400 27.32350 number of atom coordinates read : 2816 total number of charged atoms : 2667 net assigned charge : 7.000018 assigned positive charge : 412.6870 centred at (gu) : 86.69673 87.53782 79.23863 assigned negative charge : -405.6873 centred at (gu) : 87.34200 86.95733 78.54042 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 160945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30579 grid for indexing accessible points = 1.400000 m= 72173 mr = 105548 m= 23359 mr = 54094 m= 4609 mr = 16830 m= 488 mr = 2783 m= 18 mr = 264 m= 0 mr = 4 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 531 time to turn everything in is 1.460000 number of dielectric boundary points 82069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 21325 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) : 1.741541 object centre at (A) : 9.197000 -34.75400 27.32350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1261444 0.1785124 midg,1,midg; midg,igrid,midg 0.6735060 0.5118460 1,midg,midg; igrid,midg,midg 0.1276357 6.2299132E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 1.780000 now iterating at: 09:45:28 rms-change max change #iterations 9.355973 298.7800 at 10iterations 5.530248 163.5811 at 20iterations 3.224435 90.24018 at 30iterations 1.862733 51.31135 at 40iterations 1.072495 29.29881 at 50iterations 0.6152666 14.82012 at 60iterations 0.3516333 7.925388 at 70iterations 0.2015080 4.243146 at 80iterations 0.1145732 2.302841 at 90iterations 6.5252110E-02 1.496124 at 100iterations 3.7181571E-02 0.8536158 at 110iterations 2.1132249E-02 0.4466882 at 120iterations 1.2003498E-02 0.2746394 at 130iterations 6.8156300E-03 0.1557388 at 140iterations 3.8664797E-03 8.1047058E-02 at 150iterations 2.1924339E-03 4.8202515E-02 at 160iterations 1.2407185E-03 2.3635864E-02 at 170iterations 7.0420763E-04 1.3374329E-02 at 180iterations finished qdiffx linear iterations at : 09:45:45 total time elapsed so far: 17.80000 # loops : 180 mean,max change (kT/e) : 7.0420763E-04 1.3374329E-02 energy calculations done at 17.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.96000 DelPhi exited at 09:45:45 17.964u 0.516s 0:18.77 98.4% 0+0k 0+0io 0pf+0w