Sun Oct 9 15:25:46 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 15:25:46 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 = 5502 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: 0.4870307 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): 8.082999 63.17000 ymin,ymax (A): 53.68400 126.7800 zmin,zma (A): 28.99300 96.15200 x,y,z range (A): 55.08700 73.09600 67.15900 scale (grids/A): 0.4870307 object centre (A): 35.62650 90.23199 62.57250 number of atom coordinates read : 5502 total number of charged atoms : 5336 net assigned charge : 1.000036 assigned positive charge : 854.2482 centred at (gu) : 89.22466 90.30141 90.69072 assigned negative charge : -853.2559 centred at (gu) : 89.25092 90.27071 90.55280 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7759 nv = 96 ne = 84 npr = 112293 no. pairs analyzed = 112293 no. exposed pairs = 6496 no. arc points = 45287 no. surface atoms = 2181 nbur = 3321 mkacc time = 0.2400000 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 = 1.764000 m= 264 mr = 4077 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.5000000 number of dielectric boundary points 3946 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4269 ## 717 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10780 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2224828E-10 1.8090243E-10 midg,1,midg; midg,igrid,midg -2.7512282E-11 3.9413969E-11 1,midg,midg; igrid,midg,midg 3.9089749E-11 -2.0203264E-11 gauss-seidel spectral radius is 0.9784875 estimated iterations to convergence 56 setup time was (sec) 0.7200000 now iterating at: 15:25:47 rms-change max change #iterations 5.6360524E-02 7.933789 at 10iterations 3.9194990E-03 0.5298376 at 20iterations 9.0891734E-04 0.1234016 at 30iterations 3.2936354E-04 4.4048786E-02 at 40iterations 1.2713081E-04 1.7748356E-02 at 50iterations finished qdiffx linear iterations at : 15:25:50 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.2713081E-04 1.7748356E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 15:25:50 3.400u 0.149s 0:03.87 91.4% 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 15:25:50 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 = 5502 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.461092 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): 8.082999 63.17000 ymin,ymax (A): 53.68400 126.7800 zmin,zma (A): 28.99300 96.15200 x,y,z range (A): 55.08700 73.09600 67.15900 scale (grids/A): 1.461092 object centre (A): 35.62650 90.23199 62.57250 number of atom coordinates read : 5502 total number of charged atoms : 5336 net assigned charge : 1.000036 assigned positive charge : 854.2482 centred at (gu) : 87.67209 90.90246 92.06999 assigned negative charge : -853.2559 centred at (gu) : 87.75250 90.81158 91.65820 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 89746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45287 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 24050 mr = 62297 m= 1715 mr = 15818 m= 26 mr = 641 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1362 time to turn everything in is 0.6200000 number of dielectric boundary points 36781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 671 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 39335 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) : 0.4870307 object centre at (A) : 35.62650 90.23199 62.57250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2980916E-02 7.8031574E-03 midg,1,midg; midg,igrid,midg -4.0320680E-03 -1.1170155E-03 1,midg,midg; igrid,midg,midg 1.9241488E-03 4.0869790E-04 gauss-seidel spectral radius is 0.9979465 estimated iterations to convergence 175 setup time was (sec) 0.9000000 now iterating at: 15:25:51 rms-change max change #iterations 3.742511 146.7149 at 10iterations 1.475406 51.78302 at 20iterations 0.5809035 19.90243 at 30iterations 0.2295635 6.891637 at 40iterations 9.1056250E-02 2.871311 at 50iterations 3.5990212E-02 1.120787 at 60iterations 1.4366944E-02 0.4754643 at 70iterations 5.8106920E-03 0.1887897 at 80iterations 2.4731755E-03 7.9555511E-02 at 90iterations 1.1682970E-03 4.0180206E-02 at 100iterations 6.4311270E-04 2.2130966E-02 at 110iterations 4.0717362E-04 1.3204575E-02 at 120iterations finished qdiffx linear iterations at : 15:25:58 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 4.0717362E-04 1.3204575E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 15:25:58 7.249u 0.188s 0:07.74 95.8% 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 Sun Oct 9 2011 at 15:25:58 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 = 5502 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: 2.191638 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): 8.082999 63.17000 ymin,ymax (A): 53.68400 126.7800 zmin,zma (A): 28.99300 96.15200 x,y,z range (A): 55.08700 73.09600 67.15900 scale (grids/A): 2.191638 object centre (A): 35.62650 90.23199 62.57250 number of atom coordinates read : 5502 total number of charged atoms : 5336 net assigned charge : 1.000036 assigned positive charge : 854.2482 centred at (gu) : 86.50764 91.35307 93.10461 assigned negative charge : -853.2559 centred at (gu) : 86.62892 91.21735 92.48726 start vw surface at 0.2100000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 210117 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45287 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 88991 mr = 153480 m= 20086 mr = 69337 m= 2275 mr = 14290 m= 83 mr = 1300 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 4534 time to turn everything in is 1.430000 number of dielectric boundary points 83130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 42492 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) : 1.461092 object centre at (A) : 35.62650 90.23199 62.57250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2207334 0.1334199 midg,1,midg; midg,igrid,midg -0.1312663 -4.2066369E-02 1,midg,midg; igrid,midg,midg 4.4946525E-02 2.2066688E-02 gauss-seidel spectral radius is 0.9991173 estimated iterations to convergence 266 setup time was (sec) 1.740000 now iterating at: 15:26:00 rms-change max change #iterations 10.41274 297.1448 at 10iterations 5.837249 129.1058 at 20iterations 3.270310 75.06416 at 30iterations 1.814051 40.63429 at 40iterations 1.003046 21.15782 at 50iterations 0.5548363 11.50977 at 60iterations 0.3059593 5.835546 at 70iterations 0.1682104 3.341703 at 80iterations 9.2547737E-02 1.883568 at 90iterations 5.0682411E-02 0.9713430 at 100iterations 2.7835339E-02 0.5660677 at 110iterations 1.5248895E-02 0.3107796 at 120iterations 8.3406242E-03 0.1511904 at 130iterations 4.5845755E-03 8.4727287E-02 at 140iterations 2.5144757E-03 4.8921585E-02 at 150iterations 1.3856034E-03 2.4786472E-02 at 160iterations 7.6635904E-04 1.6655445E-02 at 170iterations 4.2784002E-04 7.9040527E-03 at 180iterations finished qdiffx linear iterations at : 15:26:10 total time elapsed so far: 11.62000 # loops : 180 mean,max change (kT/e) : 4.2784002E-04 7.9040527E-03 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 15:26:10 11.800u 0.205s 0:12.29 97.6% 0+0k 0+0io 0pf+0w