Sat Oct 15 11:28:25 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 Sat Oct 15 2011 at 11:28:25 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 = 3196 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: 0.5822987 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): 50.76200 111.8990 ymin,ymax (A): -18.78800 41.21000 zmin,zma (A): -34.73200 24.44300 x,y,z range (A): 61.13700 59.99800 59.17500 scale (grids/A): 0.5822987 object centre (A): 81.33050 11.21100 -5.144502 number of atom coordinates read : 3196 total number of charged atoms : 3055 net assigned charge : 6.000033 assigned positive charge : 475.7999 centred at (gu) : 88.35739 89.68592 91.51189 assigned negative charge : -469.8012 centred at (gu) : 88.26500 89.83147 91.52554 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7423 nv = 96 ne = 84 npr = 62736 no. pairs analyzed = 62736 no. exposed pairs = 4351 no. arc points = 30794 no. surface atoms = 1443 nbur = 1753 mkacc time = 0.1100000 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= 374 mr = 3800 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3018 ## 303 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2723040E-09 1.5587037E-09 midg,1,midg; midg,igrid,midg 5.4038938E-09 -2.0773836E-09 1,midg,midg; igrid,midg,midg -1.3459899E-09 2.5540727E-09 gauss-seidel spectral radius is 0.9848064 estimated iterations to convergence 67 setup time was (sec) 0.5100000 now iterating at: 11:28:27 rms-change max change #iterations 0.1038389 14.58888 at 10iterations 9.0400996E-03 1.788876 at 20iterations 1.3223488E-03 0.1910210 at 30iterations 3.5985274E-04 5.7014465E-02 at 40iterations 1.0944006E-04 1.7227173E-02 at 50iterations finished qdiffx linear iterations at : 11:28:32 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.0944006E-04 1.7227173E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 11:28:33 4.172u 0.310s 0:07.55 59.3% 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 Sat Oct 15 2011 at 11:28:34 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 = 3196 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.746896 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): 50.76200 111.8990 ymin,ymax (A): -18.78800 41.21000 zmin,zma (A): -34.73200 24.44300 x,y,z range (A): 61.13700 59.99800 59.17500 scale (grids/A): 1.746896 object centre (A): 81.33050 11.21100 -5.144502 number of atom coordinates read : 3196 total number of charged atoms : 3055 net assigned charge : 6.000033 assigned positive charge : 475.7999 centred at (gu) : 85.07146 89.05701 94.53505 assigned negative charge : -469.8012 centred at (gu) : 84.79495 89.49414 94.57658 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30794 grid for indexing accessible points = 1.400000 m= 28005 mr = 54394 m= 3802 mr = 19400 m= 158 mr = 2127 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.4100000 number of dielectric boundary points 37067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 23785 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) : 0.5822987 object centre at (A) : 81.33050 11.21100 -5.144502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6273145E-02 2.4775878E-02 midg,1,midg; midg,igrid,midg 2.0898081E-02 -1.3582369E-02 1,midg,midg; igrid,midg,midg -2.7634476E-03 6.0947742E-03 gauss-seidel spectral radius is 0.9984542 estimated iterations to convergence 202 setup time was (sec) 0.7200000 now iterating at: 11:28:35 rms-change max change #iterations 3.996681 175.0746 at 10iterations 1.763244 70.28716 at 20iterations 0.7863033 27.36322 at 30iterations 0.3508494 11.61038 at 40iterations 0.1564223 6.349945 at 50iterations 6.9828846E-02 2.234806 at 60iterations 3.1306833E-02 1.047348 at 70iterations 1.4103319E-02 0.4407768 at 80iterations 6.4752642E-03 0.2039490 at 90iterations 3.0612086E-03 0.1206207 at 100iterations 1.5046931E-03 5.6606293E-02 at 110iterations 7.9839100E-04 2.7849674E-02 at 120iterations finished qdiffx linear iterations at : 11:28:51 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 7.9839100E-04 2.7849674E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 11:28:52 9.313u 0.336s 0:18.61 51.8% 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 Sat Oct 15 2011 at 11:28:53 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 = 3196 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: 2.620344 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): 50.76200 111.8990 ymin,ymax (A): -18.78800 41.21000 zmin,zma (A): -34.73200 24.44300 x,y,z range (A): 61.13700 59.99800 59.17500 scale (grids/A): 2.620344 object centre (A): 81.33050 11.21100 -5.144502 number of atom coordinates read : 3196 total number of charged atoms : 3055 net assigned charge : 6.000033 assigned positive charge : 475.7999 centred at (gu) : 82.60717 88.58515 96.80223 assigned negative charge : -469.8012 centred at (gu) : 82.19236 89.24112 96.86478 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 187670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30794 grid for indexing accessible points = 1.400000 m= 92003 mr = 133072 m= 30941 mr = 72641 m= 6305 mr = 23689 m= 541 mr = 4335 m= 14 mr = 231 m= 0 mr = 4 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 273 time to turn everything in is 1.080000 number of dielectric boundary points 83502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 24432 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) : 1.746896 object centre at (A) : 81.33050 11.21100 -5.144502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1721270 0.1974578 midg,1,midg; midg,igrid,midg 0.2833492 -0.1987397 1,midg,midg; igrid,midg,midg 0.3822002 7.3112939E-03 gauss-seidel spectral radius is 0.9992269 estimated iterations to convergence 284 setup time was (sec) 1.370000 now iterating at: 11:28:55 rms-change max change #iterations 10.08321 287.2954 at 10iterations 5.967060 166.8433 at 20iterations 3.489569 84.70972 at 30iterations 2.027841 50.82516 at 40iterations 1.172547 30.90611 at 50iterations 0.6759041 14.07870 at 60iterations 0.3893559 7.928400 at 70iterations 0.2229863 4.455383 at 80iterations 0.1277286 2.438845 at 90iterations 7.3058352E-02 1.489030 at 100iterations 4.1716684E-02 0.8845634 at 110iterations 2.3806652E-02 0.4919052 at 120iterations 1.3599313E-02 0.2790756 at 130iterations 7.7860020E-03 0.1509666 at 140iterations 4.4516064E-03 8.1077576E-02 at 150iterations 2.5632409E-03 4.7363281E-02 at 160iterations 1.4924414E-03 3.0231476E-02 at 170iterations 8.8269822E-04 1.9229889E-02 at 180iterations finished qdiffx linear iterations at : 11:29:18 total time elapsed so far: 14.43000 # loops : 180 mean,max change (kT/e) : 8.8269822E-04 1.9229889E-02 energy calculations done at 14.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.57000 DelPhi exited at 11:29:19 14.571u 0.331s 0:26.06 57.1% 0+0k 0+0io 0pf+0w