Mon Oct 10 01:19:27 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 01:19:27 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 = 1964 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: 0.6396780 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): -6.079000 34.89100 ymin,ymax (A): -3.641000 48.38000 zmin,zma (A): -24.40600 31.24700 x,y,z range (A): 40.97000 52.02100 55.65300 scale (grids/A): 0.6396780 object centre (A): 14.40600 22.36950 3.420500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.91233 92.63090 90.15823 assigned negative charge : -284.8263 centred at (gu) : 91.03782 92.76312 90.10902 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5473 nv = 96 ne = 84 npr = 40427 no. pairs analyzed = 40427 no. exposed pairs = 2474 no. arc points = 17570 no. surface atoms = 840 nbur = 1124 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3033 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1700000 number of dielectric boundary points 2705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1738 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6815191E-10 9.1511856E-09 midg,1,midg; midg,igrid,midg 8.9912335E-09 -1.1972924E-08 1,midg,midg; igrid,midg,midg 1.2456238E-08 -7.3321318E-09 gauss-seidel spectral radius is 0.9872831 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 01:19:28 rms-change max change #iterations 0.1217185 17.09801 at 10iterations 1.1833445E-02 1.927834 at 20iterations 1.2010129E-03 0.1688271 at 30iterations 1.1571695E-04 1.7868042E-02 at 40iterations 1.1496087E-05 1.9092560E-03 at 50iterations finished qdiffx linear iterations at : 01:19:31 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.1496087E-05 1.9092560E-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 01:19:31 3.421u 0.161s 0:03.90 91.7% 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 01:19:31 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 = 1964 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: 1.919034 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): -6.079000 34.89100 ymin,ymax (A): -3.641000 48.38000 zmin,zma (A): -24.40600 31.24700 x,y,z range (A): 40.97000 52.02100 55.65300 scale (grids/A): 1.919034 object centre (A): 14.40600 22.36950 3.420500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.73711 97.89273 90.47460 assigned negative charge : -284.8263 centred at (gu) : 93.11354 98.28963 90.32719 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 58898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17570 grid for indexing accessible points = 1.400000 m= 21944 mr = 40311 m= 3485 mr = 16806 m= 164 mr = 2324 m= 1 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1490 time to turn everything in is 0.3300000 number of dielectric boundary points 24986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14437 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) : 0.6396780 object centre at (A) : 14.40600 22.36950 3.420500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7658294E-02 1.4846130E-02 midg,1,midg; midg,igrid,midg 3.5833862E-02 -8.5373279E-03 1,midg,midg; igrid,midg,midg 8.5733002E-03 -6.3734394E-03 gauss-seidel spectral radius is 0.9985773 estimated iterations to convergence 210 setup time was (sec) 0.5500000 now iterating at: 01:19:32 rms-change max change #iterations 3.587080 188.0869 at 10iterations 1.651459 63.40568 at 20iterations 0.7655173 29.56672 at 30iterations 0.3518106 12.43195 at 40iterations 0.1619758 6.003538 at 50iterations 7.4799523E-02 2.574295 at 60iterations 3.4267247E-02 1.153864 at 70iterations 1.5769472E-02 0.5323143 at 80iterations 7.2949138E-03 0.2675009 at 90iterations 3.3689605E-03 0.1255493 at 100iterations 1.5516593E-03 4.9190521E-02 at 110iterations 7.1358203E-04 2.7439117E-02 at 120iterations finished qdiffx linear iterations at : 01:19:39 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 7.1358203E-04 2.7439117E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 01:19:40 7.746u 0.172s 0:08.23 96.1% 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 Mon Oct 10 2011 at 01:19:40 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 = 1964 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: 2.878551 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): -6.079000 34.89100 ymin,ymax (A): -3.641000 48.38000 zmin,zma (A): -24.40600 31.24700 x,y,z range (A): 40.97000 52.02100 55.65300 scale (grids/A): 2.878551 object centre (A): 14.40600 22.36950 3.420500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 94.10568 101.8392 90.71194 assigned negative charge : -284.8263 centred at (gu) : 94.67039 102.4344 90.49085 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 135732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17570 grid for indexing accessible points = 1.400000 m= 69713 mr = 97459 m= 26705 mr = 57669 m= 6184 mr = 22260 m= 710 mr = 4880 m= 42 mr = 485 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 4962 time to turn everything in is 0.7900000 number of dielectric boundary points 56308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14656 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) : 1.919034 object centre at (A) : 14.40600 22.36950 3.420500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.080376 3.6650062E-02 midg,1,midg; midg,igrid,midg 0.3512362 -0.1019070 1,midg,midg; igrid,midg,midg 5.1488768E-02 -4.0722378E-02 gauss-seidel spectral radius is 0.9992306 estimated iterations to convergence 285 setup time was (sec) 1.020000 now iterating at: 01:19:41 rms-change max change #iterations 8.446212 432.2755 at 10iterations 4.846809 116.3837 at 20iterations 2.749104 59.74244 at 30iterations 1.560955 36.31656 at 40iterations 0.8848987 18.64302 at 50iterations 0.5014367 10.59332 at 60iterations 0.2842507 5.587500 at 70iterations 0.1612505 3.185120 at 80iterations 9.1551311E-02 1.834599 at 90iterations 5.1809136E-02 0.9811363 at 100iterations 2.9289687E-02 0.6386032 at 110iterations 1.6637696E-02 0.3280793 at 120iterations 9.4349114E-03 0.1971741 at 130iterations 5.3349603E-03 0.1117220 at 140iterations 3.0277057E-03 5.8135986E-02 at 150iterations 1.7200463E-03 3.3206940E-02 at 160iterations 9.7336469E-04 1.9218445E-02 at 170iterations 5.5282190E-04 1.1207581E-02 at 180iterations finished qdiffx linear iterations at : 01:19:52 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 5.5282190E-04 1.1207581E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 01:19:53 12.346u 0.205s 0:13.02 96.3% 0+0k 0+0io 0pf+0w