Sun Oct 9 23:35:19 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 Sun Oct 9 2011 at 23:35:19 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 0.5682090 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 0.5682090 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2340 net assigned charge : 1.525006 assigned positive charge : 370.4332 centred at (gu) : 88.96030 88.51730 89.40733 assigned negative charge : -368.9088 centred at (gu) : 89.04972 88.54412 89.41782 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5177 nv = 96 ne = 84 npr = 49956 no. pairs analyzed = 49956 no. exposed pairs = 3148 no. arc points = 22375 no. surface atoms = 1063 nbur = 1417 mkacc time = 8.0000006E-02 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 = 1.540000 m= 216 mr = 2632 m= 4 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2378 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6743 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7711759E-10 6.3226313E-11 midg,1,midg; midg,igrid,midg 7.5173728E-10 -8.7544805E-11 1,midg,midg; igrid,midg,midg 1.6474194E-09 -7.0157269E-10 gauss-seidel spectral radius is 0.9839790 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 23:35:19 rms-change max change #iterations 7.9223379E-02 12.60853 at 10iterations 5.7927556E-03 0.9624290 at 20iterations 4.3505241E-04 6.9858551E-02 at 30iterations 3.1294039E-05 6.1378479E-03 at 40iterations 2.3604639E-06 5.3310394E-04 at 50iterations finished qdiffx linear iterations at : 23:35:22 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.3604639E-06 5.3310394E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 23:35:23 3.418u 0.165s 0:04.00 89.2% 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 23:35:23 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 1.704627 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 1.704627 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2340 net assigned charge : 1.525006 assigned positive charge : 370.4332 centred at (gu) : 86.88042 85.55144 88.22140 assigned negative charge : -368.9088 centred at (gu) : 87.14896 85.63218 88.25328 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 56705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22375 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17169 mr = 37573 m= 1927 mr = 11837 m= 64 mr = 1036 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 2052 time to turn everything in is 0.3000000 number of dielectric boundary points 25417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 18121 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) : 0.5682090 object centre at (A) : 44.68900 9.931501 9.203000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1272955E-02 4.5435796E-03 midg,1,midg; midg,igrid,midg 1.9049067E-02 1.3883816E-02 1,midg,midg; igrid,midg,midg 5.1273531E-03 -9.3846824E-03 gauss-seidel spectral radius is 0.9982767 estimated iterations to convergence 191 setup time was (sec) 0.5100000 now iterating at: 23:35:23 rms-change max change #iterations 3.239562 177.2962 at 10iterations 1.376168 59.48314 at 20iterations 0.5878752 24.48606 at 30iterations 0.2491153 9.361968 at 40iterations 0.1057984 4.168161 at 50iterations 4.5131836E-02 1.913264 at 60iterations 1.9271290E-02 0.6828580 at 70iterations 8.1882877E-03 0.3062229 at 80iterations 3.4920333E-03 0.1325417 at 90iterations 1.4821757E-03 5.5543900E-02 at 100iterations 6.3235959E-04 2.3444176E-02 at 110iterations 2.6998881E-04 1.0428429E-02 at 120iterations finished qdiffx linear iterations at : 23:35:31 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.6998881E-04 1.0428429E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 23:35:31 7.719u 0.184s 0:08.31 94.9% 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 23:35:31 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2480 !!! WARNING: SEP 141 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.556941 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): 21.13000 68.24800 ymin,ymax (A): -21.39500 41.25800 zmin,zma (A): -19.58700 37.99300 x,y,z range (A): 47.11800 62.65300 57.58000 scale (grids/A): 2.556941 object centre (A): 44.68900 9.931501 9.203000 number of atom coordinates read : 2480 total number of charged atoms : 2340 net assigned charge : 1.525006 assigned positive charge : 370.4332 centred at (gu) : 85.32040 83.32706 87.33200 assigned negative charge : -368.9088 centred at (gu) : 85.72341 83.44821 87.37989 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 131554 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22375 grid for indexing accessible points = 1.400000 m= 59023 mr = 91875 m= 17436 mr = 46612 m= 3036 mr = 13212 m= 264 mr = 2065 m= 5 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 7247 time to turn everything in is 0.6900000 number of dielectric boundary points 57422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18712 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) : 1.704627 object centre at (A) : 44.68900 9.931501 9.203000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2252421 6.5148920E-02 midg,1,midg; midg,igrid,midg 0.4292467 0.2692390 1,midg,midg; igrid,midg,midg 0.1018634 -0.1405555 gauss-seidel spectral radius is 0.9991535 estimated iterations to convergence 271 setup time was (sec) 0.9300000 now iterating at: 23:35:32 rms-change max change #iterations 8.143213 317.3495 at 10iterations 4.531789 117.2826 at 20iterations 2.510192 58.34856 at 30iterations 1.389395 32.27061 at 40iterations 0.7716118 16.29821 at 50iterations 0.4256534 9.280691 at 60iterations 0.2351594 5.608928 at 70iterations 0.1296698 3.079698 at 80iterations 7.1517311E-02 1.598878 at 90iterations 3.9419129E-02 0.9648306 at 100iterations 2.1762811E-02 0.4766555 at 110iterations 1.1976909E-02 0.2476543 at 120iterations 6.5931347E-03 0.1509724 at 130iterations 3.6431036E-03 8.1837654E-02 at 140iterations 2.0085289E-03 4.3153763E-02 at 150iterations 1.1052381E-03 2.2832870E-02 at 160iterations 6.1025692E-04 1.3268948E-02 at 170iterations 3.3684599E-04 7.2021484E-03 at 180iterations finished qdiffx linear iterations at : 23:35:43 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 3.3684599E-04 7.2021484E-03 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 23:35:44 12.240u 0.207s 0:12.72 97.7% 0+0k 0+0io 0pf+0w