Mon Oct 10 14:02:22 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+sph2.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 = amb2.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 14:02:22 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 !!! WARNING: SEP 415 has a net charge of -0.4750 !!! WARNING: GLM 471 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6283424 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): 45.55300 102.2100 ymin,ymax (A): -24.65000 28.71400 zmin,zma (A): 1.883000 53.72200 x,y,z range (A): 56.65700 53.36400 51.83900 scale (grids/A): 0.6283424 object centre (A): 73.88150 2.032000 27.80250 number of atom coordinates read : 3277 total number of charged atoms : 3124 net assigned charge : 1.931010 assigned positive charge : 490.2247 centred at (gu) : 88.96150 88.54884 90.04804 assigned negative charge : -488.2951 centred at (gu) : 88.87397 88.56828 90.09322 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8477 nv = 96 ne = 84 npr = 68347 no. pairs analyzed = 68347 no. exposed pairs = 3663 no. arc points = 25682 no. surface atoms = 1254 nbur = 2023 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4916 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3800000 number of dielectric boundary points 3952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2499 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10461 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7610149E-09 -2.7615699E-09 midg,1,midg; midg,igrid,midg 5.6660023E-09 3.3222737E-11 1,midg,midg; igrid,midg,midg -9.2149053E-09 8.9680947E-09 gauss-seidel spectral radius is 0.9869324 estimated iterations to convergence 72 setup time was (sec) 0.6700000 now iterating at: 14:02:23 rms-change max change #iterations 0.1512935 19.28784 at 10iterations 1.4811219E-02 1.806787 at 20iterations 1.4770007E-03 0.1998920 at 30iterations 1.7046012E-04 2.2615433E-02 at 40iterations 2.8738406E-05 3.1950474E-03 at 50iterations finished qdiffx linear iterations at : 14:02:27 total time elapsed so far: 4.940000 # loops : 50 mean,max change (kT/e) : 2.8738406E-05 3.1950474E-03 energy calculations done at 4.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.110000 DelPhi exited at 14:02:28 5.120u 0.446s 0:06.14 90.5% 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 Mon Oct 10 2011 at 14:02:28 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 !!! WARNING: SEP 415 has a net charge of -0.4750 !!! WARNING: GLM 471 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.885027 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): 45.55300 102.2100 ymin,ymax (A): -24.65000 28.71400 zmin,zma (A): 1.883000 53.72200 x,y,z range (A): 56.65700 53.36400 51.83900 scale (grids/A): 1.885027 object centre (A): 73.88150 2.032000 27.80250 number of atom coordinates read : 3277 total number of charged atoms : 3124 net assigned charge : 1.931010 assigned positive charge : 490.2247 centred at (gu) : 86.88384 85.64584 90.14359 assigned negative charge : -488.2951 centred at (gu) : 86.62151 85.70449 90.27945 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 92977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25682 grid for indexing accessible points = 1.400000 m= 33581 mr = 67176 m= 4940 mr = 25128 m= 265 mr = 3045 m= 5 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1112 time to turn everything in is 0.7400000 number of dielectric boundary points 36345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24581 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) : 0.6283424 object centre at (A) : 73.88150 2.032000 27.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3931423E-02 -1.4765567E-02 midg,1,midg; midg,igrid,midg 8.1119342E-03 6.1986158E-03 1,midg,midg; igrid,midg,midg -1.8650433E-03 3.8780585E-02 gauss-seidel spectral radius is 0.9986633 estimated iterations to convergence 217 setup time was (sec) 1.090000 now iterating at: 14:02:30 rms-change max change #iterations 4.718384 173.2913 at 10iterations 2.226896 67.31268 at 20iterations 1.051211 31.20274 at 30iterations 0.4970755 15.03563 at 40iterations 0.2354337 6.481283 at 50iterations 0.1114932 3.113029 at 60iterations 5.2563321E-02 1.500427 at 70iterations 2.4848690E-02 0.7247391 at 80iterations 1.1786030E-02 0.3310699 at 90iterations 5.5749500E-03 0.1557260 at 100iterations 2.6337591E-03 8.2649231E-02 at 110iterations 1.2509617E-03 3.6432266E-02 at 120iterations finished qdiffx linear iterations at : 14:02:41 total time elapsed so far: 12.18000 # loops : 120 mean,max change (kT/e) : 1.2509617E-03 3.6432266E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 14:02:42 12.349u 0.533s 0:13.74 93.6% 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 14:02:42 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 !!! WARNING: SEP 415 has a net charge of -0.4750 !!! WARNING: GLM 471 has a net charge of -0.0940 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: 2.827541 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): 45.55300 102.2100 ymin,ymax (A): -24.65000 28.71400 zmin,zma (A): 1.883000 53.72200 x,y,z range (A): 56.65700 53.36400 51.83900 scale (grids/A): 2.827541 object centre (A): 73.88150 2.032000 27.80250 number of atom coordinates read : 3277 total number of charged atoms : 3124 net assigned charge : 1.931010 assigned positive charge : 490.2247 centred at (gu) : 85.32557 83.46861 90.21503 assigned negative charge : -488.2951 centred at (gu) : 84.93231 83.55667 90.41914 start vw surface at 0.1400000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 215412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25682 grid for indexing accessible points = 1.400000 m= 110072 mr = 162031 m= 38859 mr = 91533 m= 8723 mr = 31350 m= 1072 mr = 6500 m= 49 mr = 690 m= 0 mr = 11 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 3600 time to turn everything in is 2.020000 number of dielectric boundary points 82072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 24989 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) : 1.885027 object centre at (A) : 73.88150 2.032000 27.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3360904 -0.1337176 midg,1,midg; midg,igrid,midg -0.1799022 4.5309771E-02 1,midg,midg; igrid,midg,midg 2.8439216E-02 0.4424171 gauss-seidel spectral radius is 0.9992741 estimated iterations to convergence 293 setup time was (sec) 2.470000 now iterating at: 14:02:45 rms-change max change #iterations 11.08279 428.9810 at 10iterations 6.481344 162.7101 at 20iterations 3.773180 66.99318 at 30iterations 2.197869 37.74472 at 40iterations 1.274110 25.35615 at 50iterations 0.7388721 12.93992 at 60iterations 0.4280339 7.166672 at 70iterations 0.2475100 4.007254 at 80iterations 0.1435451 2.362186 at 90iterations 8.2868643E-02 1.516746 at 100iterations 4.7987416E-02 0.8660698 at 110iterations 2.7740611E-02 0.4513988 at 120iterations 1.6050849E-02 0.2624664 at 130iterations 9.3197906E-03 0.1534615 at 140iterations 5.3918781E-03 8.4590197E-02 at 150iterations 3.1386802E-03 4.9541473E-02 at 160iterations 1.8315854E-03 2.8168201E-02 at 170iterations 1.0764712E-03 1.7570496E-02 at 180iterations finished qdiffx linear iterations at : 14:03:04 total time elapsed so far: 21.40000 # loops : 180 mean,max change (kT/e) : 1.0764712E-03 1.7570496E-02 energy calculations done at 21.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.57000 DelPhi exited at 14:03:04 21.571u 0.541s 0:22.42 98.6% 0+0k 0+0io 0pf+0w