Tue Oct 11 03:21:28 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 Tue Oct 11 2011 at 03:21:28 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 = 3105 !!! WARNING: ASP 165 has a net charge of -0.2720 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: 0.5927603 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): 53.85100 113.9090 ymin,ymax (A): 7.2000027E-02 43.82300 zmin,zma (A): -65.17200 -10.53700 x,y,z range (A): 60.05801 43.75100 54.63499 scale (grids/A): 0.5927603 object centre (A): 83.88000 21.94750 -37.85450 number of atom coordinates read : 3105 total number of charged atoms : 2968 net assigned charge : -4.271960 assigned positive charge : 460.2130 centred at (gu) : 91.55214 90.38702 88.03559 assigned negative charge : -464.4860 centred at (gu) : 91.53951 90.41406 87.99010 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7077 nv = 96 ne = 84 npr = 64712 no. pairs analyzed = 64712 no. exposed pairs = 3807 no. arc points = 26839 no. surface atoms = 1293 nbur = 1812 mkacc time = 0.1700000 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 = 1.484000 m= 381 mr = 3888 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.3400000 number of dielectric boundary points 3534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2753 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9051 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6896487E-09 8.2853023E-11 midg,1,midg; midg,igrid,midg -4.3448964E-10 -2.5511904E-09 1,midg,midg; igrid,midg,midg -1.3000812E-09 -1.3530417E-09 gauss-seidel spectral radius is 0.9853113 estimated iterations to convergence 68 setup time was (sec) 0.6400000 now iterating at: 03:21:29 rms-change max change #iterations 0.1140094 16.11459 at 10iterations 9.4406251E-03 1.454021 at 20iterations 8.1999233E-04 0.1266365 at 30iterations 1.1190736E-04 1.7887115E-02 at 40iterations 2.9387089E-05 4.9623251E-03 at 50iterations finished qdiffx linear iterations at : 03:21:33 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 2.9387089E-05 4.9623251E-03 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 03:21:34 4.539u 0.395s 0:05.36 91.7% 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 Tue Oct 11 2011 at 03:21:34 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 = 3105 !!! WARNING: ASP 165 has a net charge of -0.2720 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: 1.778281 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): 53.85100 113.9090 ymin,ymax (A): 7.2000027E-02 43.82300 zmin,zma (A): -65.17200 -10.53700 x,y,z range (A): 60.05801 43.75100 54.63499 scale (grids/A): 1.778281 object centre (A): 83.88000 21.94750 -37.85450 number of atom coordinates read : 3105 total number of charged atoms : 2968 net assigned charge : -4.271960 assigned positive charge : 460.2130 centred at (gu) : 94.65585 91.16017 84.10596 assigned negative charge : -464.4860 centred at (gu) : 94.61815 91.24185 83.97015 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26839 grid for indexing accessible points = 1.400000 m= 28107 mr = 51835 m= 4370 mr = 21041 m= 179 mr = 2660 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1456 time to turn everything in is 0.6200000 number of dielectric boundary points 32703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23112 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) : 0.5927603 object centre at (A) : 83.88000 21.94750 -37.85450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3717372E-02 1.8028054E-02 midg,1,midg; midg,igrid,midg -1.8717767E-03 -1.0014227E-02 1,midg,midg; igrid,midg,midg -1.0101454E-02 -4.0267982E-02 gauss-seidel spectral radius is 0.9984777 estimated iterations to convergence 203 setup time was (sec) 0.9500000 now iterating at: 03:21:35 rms-change max change #iterations 4.052116 160.1370 at 10iterations 1.808412 62.56245 at 20iterations 0.8101500 29.18537 at 30iterations 0.3644643 11.44530 at 40iterations 0.1632441 5.343557 at 50iterations 7.3425680E-02 2.512462 at 60iterations 3.2989677E-02 1.141838 at 70iterations 1.4838394E-02 0.4732971 at 80iterations 6.6933353E-03 0.2073040 at 90iterations 3.0355605E-03 9.7702503E-02 at 100iterations 1.3967077E-03 4.7208786E-02 at 110iterations 6.6074845E-04 2.5613308E-02 at 120iterations finished qdiffx linear iterations at : 03:21:44 total time elapsed so far: 10.37000 # loops : 120 mean,max change (kT/e) : 6.6074845E-04 2.5613308E-02 energy calculations done at 10.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.54000 DelPhi exited at 03:21:45 10.540u 0.465s 0:11.31 97.2% 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 Oct 11 2011 at 03:21:45 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 = 3105 !!! WARNING: ASP 165 has a net charge of -0.2720 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: 2.667421 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): 53.85100 113.9090 ymin,ymax (A): 7.2000027E-02 43.82300 zmin,zma (A): -65.17200 -10.53700 x,y,z range (A): 60.05801 43.75100 54.63499 scale (grids/A): 2.667421 object centre (A): 83.88000 21.94750 -37.85450 number of atom coordinates read : 3105 total number of charged atoms : 2968 net assigned charge : -4.271960 assigned positive charge : 460.2130 centred at (gu) : 96.98357 91.73992 81.15858 assigned negative charge : -464.4860 centred at (gu) : 96.92718 91.86262 80.95505 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 174831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26839 grid for indexing accessible points = 1.400000 m= 89449 mr = 125935 m= 33973 mr = 73222 m= 7646 mr = 27694 m= 897 mr = 5655 m= 36 mr = 523 m= 0 mr = 7 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 5104 time to turn everything in is 1.620000 number of dielectric boundary points 73796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 23735 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) : 1.778281 object centre at (A) : 83.88000 21.94750 -37.85450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4238632 0.1602175 midg,1,midg; midg,igrid,midg -1.1098049E-02 -0.1108565 1,midg,midg; igrid,midg,midg -0.1180899 -0.8494824 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 1.950000 now iterating at: 03:21:47 rms-change max change #iterations 9.858760 299.1150 at 10iterations 5.705226 114.0580 at 20iterations 3.280387 70.68336 at 30iterations 1.871896 34.59052 at 40iterations 1.069727 19.42864 at 50iterations 0.6111516 13.08756 at 60iterations 0.3479066 6.909533 at 70iterations 0.1979202 3.997529 at 80iterations 0.1126363 2.052109 at 90iterations 6.3968018E-02 1.139794 at 100iterations 3.6440071E-02 0.6901288 at 110iterations 2.0711908E-02 0.3839455 at 120iterations 1.1778486E-02 0.2266989 at 130iterations 6.7088953E-03 0.1310120 at 140iterations 3.8443794E-03 7.6646805E-02 at 150iterations 2.2112601E-03 4.0450811E-02 at 160iterations 1.2922777E-03 2.6318550E-02 at 170iterations 7.7171327E-04 1.6437531E-02 at 180iterations finished qdiffx linear iterations at : 03:22:03 total time elapsed so far: 17.61000 # loops : 180 mean,max change (kT/e) : 7.7171327E-04 1.6437531E-02 energy calculations done at 17.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.77000 DelPhi exited at 03:22:04 17.774u 0.512s 0:18.67 97.9% 0+0k 0+0io 0pf+0w