Mon Oct 10 19:37:15 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 19:37:15 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 = 2667 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: 0.6034512 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): -24.12500 24.80100 ymin,ymax (A): -21.63000 34.00600 zmin,zma (A): 6.141000 65.13500 x,y,z range (A): 48.92600 55.63600 58.99400 scale (grids/A): 0.6034512 object centre (A): 0.3379993 6.188001 35.63800 number of atom coordinates read : 2667 total number of charged atoms : 2529 net assigned charge : 7.500036 assigned positive charge : 393.1636 centred at (gu) : 90.92977 87.75404 92.51283 assigned negative charge : -385.6648 centred at (gu) : 90.82387 87.77814 92.53593 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6526 nv = 96 ne = 84 npr = 53190 no. pairs analyzed = 53190 no. exposed pairs = 3594 no. arc points = 24950 no. surface atoms = 1211 nbur = 1456 mkacc time = 9.0000004E-02 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= 301 mr = 3350 m= 0 mr = 23 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.1900000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2486 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5588769E-09 4.4518265E-09 midg,1,midg; midg,igrid,midg 7.3643647E-09 1.5828614E-09 1,midg,midg; igrid,midg,midg -5.8161054E-10 9.4481463E-09 gauss-seidel spectral radius is 0.9857981 estimated iterations to convergence 69 setup time was (sec) 0.3700000 now iterating at: 19:37:16 rms-change max change #iterations 0.1096030 17.73850 at 10iterations 9.5671527E-03 1.454565 at 20iterations 8.3108695E-04 0.1563854 at 30iterations 7.7052398E-05 1.2222290E-02 at 40iterations 7.8913381E-06 1.2722015E-03 at 50iterations finished qdiffx linear iterations at : 19:37:19 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 7.8913381E-06 1.2722015E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 19:37:19 3.352u 0.199s 0:04.03 87.8% 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 19:37:19 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 = 2667 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.810354 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): -24.12500 24.80100 ymin,ymax (A): -21.63000 34.00600 zmin,zma (A): 6.141000 65.13500 x,y,z range (A): 48.92600 55.63600 58.99400 scale (grids/A): 1.810354 object centre (A): 0.3379993 6.188001 35.63800 number of atom coordinates read : 2667 total number of charged atoms : 2529 net assigned charge : 7.500036 assigned positive charge : 393.1636 centred at (gu) : 92.78872 83.26149 97.53775 assigned negative charge : -385.6648 centred at (gu) : 92.47144 83.33435 97.60782 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24950 grid for indexing accessible points = 1.400000 m= 23516 mr = 47731 m= 3108 mr = 16436 m= 137 mr = 1707 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 0.3500000 number of dielectric boundary points 32125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19773 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) : 0.6034512 object centre at (A) : 0.3379993 6.188001 35.63800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1723611E-02 3.3399776E-02 midg,1,midg; midg,igrid,midg -3.2722591E-03 3.6545177E-03 1,midg,midg; igrid,midg,midg 1.5623956E-02 2.2155061E-02 gauss-seidel spectral radius is 0.9985002 estimated iterations to convergence 205 setup time was (sec) 0.5600000 now iterating at: 19:37:20 rms-change max change #iterations 3.788933 184.6993 at 10iterations 1.695555 68.11661 at 20iterations 0.7667881 28.68857 at 30iterations 0.3450295 11.22074 at 40iterations 0.1556497 5.103399 at 50iterations 7.0230149E-02 2.384271 at 60iterations 3.1556077E-02 1.002487 at 70iterations 1.4305727E-02 0.4650412 at 80iterations 6.4781965E-03 0.2236691 at 90iterations 2.9200553E-03 9.2259407E-02 at 100iterations 1.3190093E-03 4.5711517E-02 at 110iterations 5.9735659E-04 1.8407822E-02 at 120iterations finished qdiffx linear iterations at : 19:37:27 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 5.9735659E-04 1.8407822E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 19:37:28 7.897u 0.216s 0:08.64 93.7% 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 19:37:28 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 = 2667 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: 2.715530 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): -24.12500 24.80100 ymin,ymax (A): -21.63000 34.00600 zmin,zma (A): 6.141000 65.13500 x,y,z range (A): 48.92600 55.63600 58.99400 scale (grids/A): 2.715530 object centre (A): 0.3379993 6.188001 35.63800 number of atom coordinates read : 2667 total number of charged atoms : 2529 net assigned charge : 7.500036 assigned positive charge : 393.1636 centred at (gu) : 94.18284 79.89209 101.3066 assigned negative charge : -385.6648 centred at (gu) : 93.70718 80.00148 101.4116 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 165393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24950 grid for indexing accessible points = 1.400000 m= 77897 mr = 117113 m= 25545 mr = 61457 m= 5159 mr = 19675 m= 575 mr = 3580 m= 23 mr = 332 m= 0 mr = 9 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 1235 time to turn everything in is 0.8700000 number of dielectric boundary points 72426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 20228 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) : 1.810354 object centre at (A) : 0.3379993 6.188001 35.63800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3712194 0.7864528 midg,1,midg; midg,igrid,midg -7.7297784E-02 0.1096343 1,midg,midg; igrid,midg,midg 0.2922746 0.1578810 gauss-seidel spectral radius is 0.9992323 estimated iterations to convergence 285 setup time was (sec) 1.100000 now iterating at: 19:37:29 rms-change max change #iterations 9.428165 291.7696 at 10iterations 5.527290 149.0133 at 20iterations 3.213517 67.99993 at 30iterations 1.853565 37.26089 at 40iterations 1.068878 22.80186 at 50iterations 0.6136695 13.12350 at 60iterations 0.3513376 8.168219 at 70iterations 0.2010032 3.969885 at 80iterations 0.1149256 2.472924 at 90iterations 6.5424800E-02 1.324718 at 100iterations 3.7351575E-02 0.6945848 at 110iterations 2.1248180E-02 0.4342308 at 120iterations 1.2119548E-02 0.2238563 at 130iterations 6.9038938E-03 0.1343307 at 140iterations 3.9338856E-03 7.7896118E-02 at 150iterations 2.2414317E-03 4.2419910E-02 at 160iterations 1.2752477E-03 2.4345398E-02 at 170iterations 7.2922523E-04 1.3330460E-02 at 180iterations finished qdiffx linear iterations at : 19:37:41 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 7.2922523E-04 1.3330460E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 19:37:42 12.518u 0.223s 0:13.54 94.0% 0+0k 0+0io 0pf+0w