Sun Oct 9 21:17:20 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 21:17:20 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 = 3193 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6091301 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): 45.34900 98.29600 ymin,ymax (A): 3.181000 61.62500 zmin,zma (A): 15.04500 67.16500 x,y,z range (A): 52.94700 58.44400 52.12000 scale (grids/A): 0.6091301 object centre (A): 71.82249 32.40300 41.10500 number of atom coordinates read : 3193 total number of charged atoms : 3138 net assigned charge : 5.500020 assigned positive charge : 498.7086 centred at (gu) : 90.24362 87.57465 90.63272 assigned negative charge : -493.2100 centred at (gu) : 90.15923 87.49550 90.63532 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8162 nv = 96 ne = 84 npr = 59246 no. pairs analyzed = 59246 no. exposed pairs = 4397 no. arc points = 32181 no. surface atoms = 1448 nbur = 1745 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 4109 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3900000 number of dielectric boundary points 4470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3258 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9789133E-09 3.5561394E-09 midg,1,midg; midg,igrid,midg -2.9654958E-09 4.7061985E-09 1,midg,midg; igrid,midg,midg -1.8106019E-09 8.8082128E-09 gauss-seidel spectral radius is 0.9861150 estimated iterations to convergence 70 setup time was (sec) 0.6700000 now iterating at: 21:17:21 rms-change max change #iterations 0.1278306 17.72133 at 10iterations 1.1177058E-02 1.698845 at 20iterations 1.0002553E-03 0.1352737 at 30iterations 8.9524758E-05 1.2704849E-02 at 40iterations 9.1162519E-06 1.3265610E-03 at 50iterations finished qdiffx linear iterations at : 21:17:25 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 9.1162519E-06 1.3265610E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 21:17:25 4.118u 0.260s 0:04.69 93.1% 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 21:17:25 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 = 3193 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.827390 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): 45.34900 98.29600 ymin,ymax (A): 3.181000 61.62500 zmin,zma (A): 15.04500 67.16500 x,y,z range (A): 52.94700 58.44400 52.12000 scale (grids/A): 1.827390 object centre (A): 71.82249 32.40300 41.10500 number of atom coordinates read : 3193 total number of charged atoms : 3138 net assigned charge : 5.500020 assigned positive charge : 498.7086 centred at (gu) : 90.73032 82.72296 91.89705 assigned negative charge : -493.2100 centred at (gu) : 90.47705 82.48623 91.90555 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32181 grid for indexing accessible points = 1.400000 m= 29918 mr = 57973 m= 4281 mr = 20585 m= 237 mr = 2355 m= 3 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1541 time to turn everything in is 0.7800000 number of dielectric boundary points 41386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 24545 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) : 0.6091301 object centre at (A) : 71.82249 32.40300 41.10500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4527600E-03 -1.3015136E-03 midg,1,midg; midg,igrid,midg 4.0363818E-02 2.7934665E-02 1,midg,midg; igrid,midg,midg -1.2027658E-02 1.3892070E-02 gauss-seidel spectral radius is 0.9986036 estimated iterations to convergence 212 setup time was (sec) 1.080000 now iterating at: 21:17:26 rms-change max change #iterations 4.455606 178.4965 at 10iterations 2.063253 65.94494 at 20iterations 0.9540528 30.17445 at 30iterations 0.4405029 14.70283 at 40iterations 0.2041340 6.493836 at 50iterations 9.4581001E-02 2.836469 at 60iterations 4.3641366E-02 1.436195 at 70iterations 2.0289894E-02 0.6436186 at 80iterations 9.4054667E-03 0.2798190 at 90iterations 4.3660104E-03 0.1342697 at 100iterations 2.0189646E-03 5.9745789E-02 at 110iterations 9.4070064E-04 2.8860092E-02 at 120iterations finished qdiffx linear iterations at : 21:17:35 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 9.4070064E-04 2.8860092E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 21:17:35 9.674u 0.289s 0:10.32 96.4% 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 21:17:35 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 = 3193 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.741086 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): 45.34900 98.29600 ymin,ymax (A): 3.181000 61.62500 zmin,zma (A): 15.04500 67.16500 x,y,z range (A): 52.94700 58.44400 52.12000 scale (grids/A): 2.741086 object centre (A): 71.82249 32.40300 41.10500 number of atom coordinates read : 3193 total number of charged atoms : 3138 net assigned charge : 5.500020 assigned positive charge : 498.7086 centred at (gu) : 91.09525 79.08414 92.84531 assigned negative charge : -493.2100 centred at (gu) : 90.71546 78.72931 92.85821 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 203705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32181 grid for indexing accessible points = 1.400000 m= 97763 mr = 141720 m= 33111 mr = 76919 m= 7442 mr = 25279 m= 1009 mr = 5150 m= 63 mr = 645 m= 0 mr = 24 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 5574 time to turn everything in is 1.950000 number of dielectric boundary points 93356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 25101 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) : 1.827390 object centre at (A) : 71.82249 32.40300 41.10500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1081661E-02 -0.1434329 midg,1,midg; midg,igrid,midg 0.3599488 0.3306035 1,midg,midg; igrid,midg,midg -0.1682627 0.1742772 gauss-seidel spectral radius is 0.9992782 estimated iterations to convergence 294 setup time was (sec) 2.290000 now iterating at: 21:17:38 rms-change max change #iterations 10.87699 309.1396 at 10iterations 6.523716 151.8889 at 20iterations 3.862849 106.6445 at 30iterations 2.274488 68.81673 at 40iterations 1.337348 29.24997 at 50iterations 0.7841439 15.83763 at 60iterations 0.4574452 9.203321 at 70iterations 0.2670697 5.096185 at 80iterations 0.1551425 2.869785 at 90iterations 9.0313464E-02 1.709039 at 100iterations 5.2525043E-02 0.9241476 at 110iterations 3.0529819E-02 0.5869064 at 120iterations 1.7724197E-02 0.3088765 at 130iterations 1.0303229E-02 0.1771936 at 140iterations 5.9726527E-03 0.1164131 at 150iterations 3.4646040E-03 5.9125900E-02 at 160iterations 2.0087145E-03 3.6482811E-02 at 170iterations 1.1637363E-03 2.1070480E-02 at 180iterations finished qdiffx linear iterations at : 21:17:52 total time elapsed so far: 16.45000 # loops : 180 mean,max change (kT/e) : 1.1637363E-03 2.1070480E-02 energy calculations done at 16.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.63000 DelPhi exited at 21:17:53 16.628u 0.325s 0:17.27 98.0% 0+0k 0+0io 0pf+0w