Mon Oct 10 17:03:42 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 Mon Oct 10 2011 at 17:03:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4743 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5126728 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): -18.82000 37.65600 ymin,ymax (A): -30.70400 35.16200 zmin,zma (A): -4.103000 65.33700 x,y,z range (A): 56.47600 65.86600 69.43999 scale (grids/A): 0.5126728 object centre (A): 9.418001 2.229001 30.61700 number of atom coordinates read : 4743 total number of charged atoms : 4497 net assigned charge : 4.800026 assigned positive charge : 711.7314 centred at (gu) : 90.13469 90.39998 88.28024 assigned negative charge : -706.9359 centred at (gu) : 90.01767 90.43671 88.26955 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7955 nv = 96 ne = 84 npr = 95318 no. pairs analyzed = 95318 no. exposed pairs = 6060 no. arc points = 42451 no. surface atoms = 2025 nbur = 2718 mkacc time = 0.2500000 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 = 1.652000 m= 274 mr = 4086 m= 0 mr = 6 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4040 ## 576 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 10541 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9499115E-11 6.7621117E-11 midg,1,midg; midg,igrid,midg 1.5973303E-10 -3.1577341E-11 1,midg,midg; igrid,midg,midg -2.4786209E-10 4.1154447E-10 gauss-seidel spectral radius is 0.9805440 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 17:03:44 rms-change max change #iterations 6.7838281E-02 11.08354 at 10iterations 3.9833351E-03 0.5848484 at 20iterations 4.1486102E-04 5.9816599E-02 at 30iterations 1.3099333E-04 1.9457579E-02 at 40iterations 5.0516301E-05 7.6924562E-03 at 50iterations finished qdiffx linear iterations at : 17:03:47 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 5.0516301E-05 7.6924562E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.960000 DelPhi exited at 17:03:48 3.960u 0.402s 0:05.70 76.4% 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 Mon Oct 10 2011 at 17:03:48 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4743 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.538019 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): -18.82000 37.65600 ymin,ymax (A): -30.70400 35.16200 zmin,zma (A): -4.103000 65.33700 x,y,z range (A): 56.47600 65.86600 69.43999 scale (grids/A): 1.538019 object centre (A): 9.418001 2.229001 30.61700 number of atom coordinates read : 4743 total number of charged atoms : 4497 net assigned charge : 4.800026 assigned positive charge : 711.7314 centred at (gu) : 90.40277 91.19853 84.83927 assigned negative charge : -706.9359 centred at (gu) : 90.05287 91.30975 84.80847 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 90298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42451 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26182 mr = 61897 m= 2332 mr = 17345 m= 48 mr = 943 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.7100000 number of dielectric boundary points 38676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 535 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 33892 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) : 0.5126728 object centre at (A) : 9.418001 2.229001 30.61700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6556597E-03 1.9092627E-02 midg,1,midg; midg,igrid,midg -8.7606668E-04 -1.2467487E-02 1,midg,midg; igrid,midg,midg -1.6674462E-03 1.1882710E-02 gauss-seidel spectral radius is 0.9981320 estimated iterations to convergence 184 setup time was (sec) 0.9900000 now iterating at: 17:03:49 rms-change max change #iterations 3.788057 143.3362 at 10iterations 1.558341 58.43054 at 20iterations 0.6411275 19.00242 at 30iterations 0.2642217 8.386803 at 40iterations 0.1088183 4.188503 at 50iterations 4.5080543E-02 1.333561 at 60iterations 1.8566273E-02 0.5920219 at 70iterations 7.6764487E-03 0.2399917 at 80iterations 3.1699184E-03 0.1090260 at 90iterations 1.3120361E-03 4.2519093E-02 at 100iterations 5.4300966E-04 1.6557693E-02 at 110iterations 2.2569778E-04 6.7839622E-03 at 120iterations finished qdiffx linear iterations at : 17:03:57 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 2.2569778E-04 6.7839622E-03 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.870000 DelPhi exited at 17:03:59 8.876u 0.443s 0:11.24 82.8% 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 Mon Oct 10 2011 at 17:04:01 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4743 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.307028 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): -18.82000 37.65600 ymin,ymax (A): -30.70400 35.16200 zmin,zma (A): -4.103000 65.33700 x,y,z range (A): 56.47600 65.86600 69.43999 scale (grids/A): 2.307028 object centre (A): 9.418001 2.229001 30.61700 number of atom coordinates read : 4743 total number of charged atoms : 4497 net assigned charge : 4.800026 assigned positive charge : 711.7314 centred at (gu) : 90.60374 91.79729 82.25855 assigned negative charge : -706.9359 centred at (gu) : 90.07911 91.96457 82.21251 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 210191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42451 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94362 mr = 152043 m= 23869 mr = 73611 m= 3271 mr = 16906 m= 201 mr = 1910 m= 0 mr = 59 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 197 time to turn everything in is 1.770000 number of dielectric boundary points 87365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 35887 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) : 1.538019 object centre at (A) : 9.418001 2.229001 30.61700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1418048 0.4802924 midg,1,midg; midg,igrid,midg -0.1439498 -0.3047402 1,midg,midg; igrid,midg,midg -1.5281430E-02 0.1802277 gauss-seidel spectral radius is 0.9991696 estimated iterations to convergence 274 setup time was (sec) 2.090000 now iterating at: 17:04:03 rms-change max change #iterations 10.25268 250.0590 at 10iterations 5.894466 165.5650 at 20iterations 3.358231 81.01938 at 30iterations 1.901923 40.35777 at 40iterations 1.074893 21.85693 at 50iterations 0.6047111 12.63490 at 60iterations 0.3397378 6.335934 at 70iterations 0.1905860 4.230698 at 80iterations 0.1068376 2.221580 at 90iterations 5.9594590E-02 1.225964 at 100iterations 3.3308659E-02 0.6905518 at 110iterations 1.8577699E-02 0.4290543 at 120iterations 1.0357826E-02 0.1985445 at 130iterations 5.7817893E-03 0.1165504 at 140iterations 3.2216553E-03 6.2534571E-02 at 150iterations 1.7938158E-03 3.6344528E-02 at 160iterations 9.9939993E-04 1.8362045E-02 at 170iterations 5.5695372E-04 1.0314941E-02 at 180iterations finished qdiffx linear iterations at : 17:04:17 total time elapsed so far: 15.54000 # loops : 180 mean,max change (kT/e) : 5.5695372E-04 1.0314941E-02 energy calculations done at 15.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.72000 DelPhi exited at 17:04:18 15.727u 0.460s 0:17.01 95.1% 0+0k 0+0io 0pf+0w