Sat Oct 8 15:46:39 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 8 2011 at 15:46:39 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 = 2452 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6479442 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): -45.36600 2.639000 ymin,ymax (A): 3.740000 50.00500 zmin,zma (A): -18.54700 36.39600 x,y,z range (A): 48.00500 46.26500 54.94300 scale (grids/A): 0.6479442 object centre (A): -21.36350 26.87250 8.924500 number of atom coordinates read : 2452 total number of charged atoms : 2385 net assigned charge : 2.000002 assigned positive charge : 368.0929 centred at (gu) : 88.72488 91.08923 90.64388 assigned negative charge : -366.0937 centred at (gu) : 88.67480 90.91991 90.73910 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7132 nv = 96 ne = 84 npr = 48207 no. pairs analyzed = 48207 no. exposed pairs = 3109 no. arc points = 21421 no. surface atoms = 1058 nbur = 1394 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 440 mr = 4014 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2101 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8422 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4284002E-08 -1.0948084E-08 midg,1,midg; midg,igrid,midg -1.5674216E-08 3.3083204E-08 1,midg,midg; igrid,midg,midg -4.3811217E-09 7.9104154E-09 gauss-seidel spectral radius is 0.9876477 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 15:46:40 rms-change max change #iterations 0.1470983 25.12762 at 10iterations 1.5093549E-02 2.020264 at 20iterations 1.5893055E-03 0.1997375 at 30iterations 1.9500073E-04 2.7866364E-02 at 40iterations 3.5281180E-05 4.8376918E-03 at 50iterations finished qdiffx linear iterations at : 15:46:42 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 3.5281180E-05 4.8376918E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 15:46:43 3.214u 0.154s 0:03.69 91.0% 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 8 2011 at 15:46:43 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 = 2452 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.943833 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): -45.36600 2.639000 ymin,ymax (A): 3.740000 50.00500 zmin,zma (A): -18.54700 36.39600 x,y,z range (A): 48.00500 46.26500 54.94300 scale (grids/A): 1.943833 object centre (A): -21.36350 26.87250 8.924500 number of atom coordinates read : 2452 total number of charged atoms : 2385 net assigned charge : 2.000002 assigned positive charge : 368.0929 centred at (gu) : 86.17411 93.26707 91.93112 assigned negative charge : -366.0937 centred at (gu) : 86.02429 92.75964 92.21727 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21421 grid for indexing accessible points = 1.400000 m= 28880 mr = 53851 m= 5249 mr = 21620 m= 329 mr = 3601 m= 6 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 742 time to turn everything in is 0.5500000 number of dielectric boundary points 31958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18811 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) : 0.6479442 object centre at (A) : -21.36350 26.87250 8.924500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8258607E-02 -1.8005678E-02 midg,1,midg; midg,igrid,midg -6.1601796E-03 2.9887607E-02 1,midg,midg; igrid,midg,midg -5.5000115E-02 2.1109192E-03 gauss-seidel spectral radius is 0.9986765 estimated iterations to convergence 218 setup time was (sec) 0.8200000 now iterating at: 15:46:44 rms-change max change #iterations 4.307213 177.6268 at 10iterations 2.041199 88.09944 at 20iterations 0.9681400 30.99897 at 30iterations 0.4609918 16.04654 at 40iterations 0.2185873 7.166321 at 50iterations 0.1039836 3.160145 at 60iterations 4.9342830E-02 1.463905 at 70iterations 2.3396185E-02 0.7976818 at 80iterations 1.1113112E-02 0.3470078 at 90iterations 5.2774483E-03 0.1699371 at 100iterations 2.5105400E-03 8.1437111E-02 at 110iterations 1.1977592E-03 3.5877228E-02 at 120iterations finished qdiffx linear iterations at : 15:46:50 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 1.1977592E-03 3.5877228E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 15:46:50 7.008u 0.177s 0:07.47 95.9% 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 8 2011 at 15:46:50 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 = 2452 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: 2.915749 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): -45.36600 2.639000 ymin,ymax (A): 3.740000 50.00500 zmin,zma (A): -18.54700 36.39600 x,y,z range (A): 48.00500 46.26500 54.94300 scale (grids/A): 2.915749 object centre (A): -21.36350 26.87250 8.924500 number of atom coordinates read : 2452 total number of charged atoms : 2385 net assigned charge : 2.000002 assigned positive charge : 368.0929 centred at (gu) : 84.26108 94.90059 92.89666 assigned negative charge : -366.0937 centred at (gu) : 84.03639 94.13937 93.32587 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 177398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21421 grid for indexing accessible points = 1.400000 m= 91957 mr = 130342 m= 35720 mr = 75841 m= 9914 mr = 29312 m= 1513 mr = 7892 m= 121 mr = 1095 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 2654 time to turn everything in is 1.370000 number of dielectric boundary points 72068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 19080 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) : 1.943833 object centre at (A) : -21.36350 26.87250 8.924500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3002098 -0.2422551 midg,1,midg; midg,igrid,midg -9.0422876E-02 0.2257619 1,midg,midg; igrid,midg,midg -0.6747464 3.4719255E-02 gauss-seidel spectral radius is 0.9992725 estimated iterations to convergence 293 setup time was (sec) 1.650000 now iterating at: 15:46:52 rms-change max change #iterations 10.08246 500.7406 at 10iterations 5.946152 154.1431 at 20iterations 3.494375 88.29670 at 30iterations 2.048349 40.41638 at 40iterations 1.198901 22.18026 at 50iterations 0.6974105 12.98445 at 60iterations 0.4062850 7.265913 at 70iterations 0.2357167 4.468590 at 80iterations 0.1367327 2.517921 at 90iterations 7.9386301E-02 1.551920 at 100iterations 4.6067160E-02 0.8882732 at 110iterations 2.6648408E-02 0.4925079 at 120iterations 1.5429542E-02 0.2939644 at 130iterations 8.9463191E-03 0.1595993 at 140iterations 5.1784059E-03 8.7697029E-02 at 150iterations 2.9985586E-03 5.0892830E-02 at 160iterations 1.7517492E-03 3.7223816E-02 at 170iterations 1.0281056E-03 1.8426895E-02 at 180iterations finished qdiffx linear iterations at : 15:47:02 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 1.0281056E-03 1.8426895E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 15:47:02 11.526u 0.218s 0:12.05 97.3% 0+0k 0+0io 0pf+0w