Sun Oct 9 19:24:05 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 Sun Oct 9 2011 at 19:24:05 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5113 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5482575 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): 3.236000 68.16900 ymin,ymax (A): -8.569000 53.47100 zmin,zma (A): -1.199000 62.04500 x,y,z range (A): 64.93300 62.04000 63.24400 scale (grids/A): 0.5482575 object centre (A): 35.70250 22.45100 30.42300 number of atom coordinates read : 5113 total number of charged atoms : 4965 net assigned charge : 0.6210455 assigned positive charge : 782.7236 centred at (gu) : 87.85899 89.13194 89.27883 assigned negative charge : -782.1087 centred at (gu) : 87.72391 89.18153 89.25438 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 10033 nv = 96 ne = 84 npr = 103757 no. pairs analyzed = 103757 no. exposed pairs = 6049 no. arc points = 40898 no. surface atoms = 2061 nbur = 3052 mkacc time = 0.2300000 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 = 1.568000 m= 412 mr = 5696 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4126 ## 476 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 13169 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7524527E-10 3.2456704E-10 midg,1,midg; midg,igrid,midg 8.7411656E-10 -4.4211937E-10 1,midg,midg; igrid,midg,midg -2.8539082E-09 1.0352573E-09 gauss-seidel spectral radius is 0.9829988 estimated iterations to convergence 63 setup time was (sec) 0.7700000 now iterating at: 19:24:06 rms-change max change #iterations 0.1032949 15.29336 at 10iterations 9.6255168E-03 1.237259 at 20iterations 3.0393319E-03 0.3449249 at 30iterations 1.4561154E-03 0.1590543 at 40iterations 7.1978039E-04 8.3729267E-02 at 50iterations finished qdiffx linear iterations at : 19:24:10 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 7.1978039E-04 8.3729267E-02 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 19:24:11 4.555u 0.302s 0:05.13 94.5% 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 Sun Oct 9 2011 at 19:24:11 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5113 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.644772 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): 3.236000 68.16900 ymin,ymax (A): -8.569000 53.47100 zmin,zma (A): -1.199000 62.04500 x,y,z range (A): 64.93300 62.04000 63.24400 scale (grids/A): 1.644772 object centre (A): 35.70250 22.45100 30.42300 number of atom coordinates read : 5113 total number of charged atoms : 4965 net assigned charge : 0.6210455 assigned positive charge : 782.7236 centred at (gu) : 83.57552 87.39411 87.83505 assigned negative charge : -782.1087 centred at (gu) : 83.17169 87.54453 87.76331 start vw surface at 0.2500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 112086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40898 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38388 mr = 81140 m= 4502 mr = 27667 m= 124 mr = 2368 m= 0 mr = 6 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 43919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 382 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 38094 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) : 0.5482575 object centre at (A) : 35.70250 22.45100 30.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2854278E-02 -1.7495403E-02 midg,1,midg; midg,igrid,midg 1.8071892E-02 7.1737971E-03 1,midg,midg; igrid,midg,midg -2.3602247E-02 2.3744132E-02 gauss-seidel spectral radius is 0.9984057 estimated iterations to convergence 199 setup time was (sec) 1.320000 now iterating at: 19:24:12 rms-change max change #iterations 4.714435 178.5348 at 10iterations 2.077526 60.58244 at 20iterations 0.9168485 26.90777 at 30iterations 0.4044351 11.93584 at 40iterations 0.1793579 5.133163 at 50iterations 7.9388700E-02 2.278381 at 60iterations 3.5780732E-02 0.9996643 at 70iterations 1.6465789E-02 0.4846954 at 80iterations 8.2226554E-03 0.2783432 at 90iterations 4.6611070E-03 0.1197262 at 100iterations 3.0379230E-03 8.1991196E-02 at 110iterations 2.1969383E-03 5.2581787E-02 at 120iterations finished qdiffx linear iterations at : 19:24:21 total time elapsed so far: 10.42000 # loops : 120 mean,max change (kT/e) : 2.1969383E-03 5.2581787E-02 energy calculations done at 10.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 19:24:22 10.591u 0.359s 0:11.22 97.5% 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 Sun Oct 9 2011 at 19:24:22 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5113 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.467159 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): 3.236000 68.16900 ymin,ymax (A): -8.569000 53.47100 zmin,zma (A): -1.199000 62.04500 x,y,z range (A): 64.93300 62.04000 63.24400 scale (grids/A): 2.467159 object centre (A): 35.70250 22.45100 30.42300 number of atom coordinates read : 5113 total number of charged atoms : 4965 net assigned charge : 0.6210455 assigned positive charge : 782.7236 centred at (gu) : 80.36311 86.09070 86.75224 assigned negative charge : -782.1087 centred at (gu) : 79.75764 86.31686 86.64500 start vw surface at 0.1900000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 260781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40898 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 130861 mr = 197882 m= 40757 mr = 106539 m= 7073 mr = 31383 m= 544 mr = 4790 m= 4 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.150000 number of dielectric boundary points 99185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 39683 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) : 1.644772 object centre at (A) : 35.70250 22.45100 30.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3540181 -0.3950290 midg,1,midg; midg,igrid,midg 9.7185150E-02 -1.2247755E-02 1,midg,midg; igrid,midg,midg -0.4750771 0.3602293 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 2.540000 now iterating at: 19:24:25 rms-change max change #iterations 12.01364 320.6276 at 10iterations 7.075794 139.6242 at 20iterations 4.123877 83.10866 at 30iterations 2.404626 49.23911 at 40iterations 1.392817 26.30046 at 50iterations 0.8069397 14.67062 at 60iterations 0.4656178 7.666360 at 70iterations 0.2680298 4.186076 at 80iterations 0.1547606 2.469710 at 90iterations 8.9137405E-02 1.392242 at 100iterations 5.1473957E-02 0.8172379 at 110iterations 2.9802829E-02 0.5168409 at 120iterations 1.7474722E-02 0.2985916 at 130iterations 1.0479167E-02 0.1784210 at 140iterations 6.5609817E-03 0.1153944 at 150iterations 4.3557519E-03 8.0413580E-02 at 160iterations 3.1165907E-03 5.2957237E-02 at 170iterations 2.3912198E-03 3.7017822E-02 at 180iterations finished qdiffx linear iterations at : 19:24:40 total time elapsed so far: 18.26000 # loops : 180 mean,max change (kT/e) : 2.3912198E-03 3.7017822E-02 energy calculations done at 18.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.44000 DelPhi exited at 19:24:41 18.445u 0.372s 0:19.09 98.5% 0+0k 0+0io 0pf+0w