Mon Oct 10 17:15:30 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 17:15:30 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5103943 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): -18.35400 36.66900 ymin,ymax (A): -32.31200 35.08000 zmin,zma (A): -3.998000 65.75200 x,y,z range (A): 55.02300 67.39200 69.75000 scale (grids/A): 0.5103943 object centre (A): 9.157501 1.384001 30.87700 number of atom coordinates read : 4786 total number of charged atoms : 4582 net assigned charge : 3.400030 assigned positive charge : 723.3722 centred at (gu) : 90.23179 90.63523 88.30809 assigned negative charge : -719.9769 centred at (gu) : 90.14095 90.66595 88.36288 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7768 nv = 96 ne = 84 npr = 96931 no. pairs analyzed = 96931 no. exposed pairs = 6267 no. arc points = 43042 no. surface atoms = 2079 nbur = 2707 mkacc time = 0.2200000 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 = 1.680000 m= 299 mr = 3909 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4127 ## 600 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 10513 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9168146E-10 -6.1702740E-11 midg,1,midg; midg,igrid,midg 1.0501217E-10 -4.1564332E-11 1,midg,midg; igrid,midg,midg -1.8083478E-10 2.9444416E-10 gauss-seidel spectral radius is 0.9803686 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:15:31 rms-change max change #iterations 6.7211330E-02 10.56231 at 10iterations 3.8783553E-03 0.5590973 at 20iterations 3.6246446E-04 5.2144051E-02 at 30iterations 1.0636042E-04 1.5219212E-02 at 40iterations 4.3281616E-05 7.1167946E-03 at 50iterations finished qdiffx linear iterations at : 17:15:33 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.3281616E-05 7.1167946E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 17:15:34 3.512u 0.140s 0:04.05 90.1% 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 Mon Oct 10 2011 at 17:15:34 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.531183 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): -18.35400 36.66900 ymin,ymax (A): -32.31200 35.08000 zmin,zma (A): -3.998000 65.75200 x,y,z range (A): 55.02300 67.39200 69.75000 scale (grids/A): 1.531183 object centre (A): 9.157501 1.384001 30.87700 number of atom coordinates read : 4786 total number of charged atoms : 4582 net assigned charge : 3.400030 assigned positive charge : 723.3722 centred at (gu) : 90.69382 91.90463 84.92282 assigned negative charge : -719.9769 centred at (gu) : 90.42260 91.99786 85.08834 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 88164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43042 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25404 mr = 59817 m= 2274 mr = 16543 m= 44 mr = 897 m= 0 mr = 1 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.6800000 number of dielectric boundary points 38628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 546 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 34485 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) : 0.5103943 object centre at (A) : 9.157501 1.384001 30.87700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9728371E-03 -5.4927976E-03 midg,1,midg; midg,igrid,midg -1.8891158E-03 -5.6150127E-03 1,midg,midg; igrid,midg,midg -1.2860205E-03 1.0554035E-02 gauss-seidel spectral radius is 0.9981118 estimated iterations to convergence 183 setup time was (sec) 0.9900000 now iterating at: 17:15:35 rms-change max change #iterations 3.792244 156.0827 at 10iterations 1.555827 55.99643 at 20iterations 0.6367835 21.18237 at 30iterations 0.2619711 9.355507 at 40iterations 0.1073240 4.367884 at 50iterations 4.4104300E-02 1.479155 at 60iterations 1.8102407E-02 0.6330261 at 70iterations 7.4635642E-03 0.2386665 at 80iterations 3.0810924E-03 0.1033125 at 90iterations 1.2768012E-03 4.6966553E-02 at 100iterations 5.3729780E-04 1.7866135E-02 at 110iterations 2.3767068E-04 8.2740784E-03 at 120iterations finished qdiffx linear iterations at : 17:15:43 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 2.3767068E-04 8.2740784E-03 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 17:15:43 8.495u 0.245s 0:09.21 94.7% 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 17:15:43 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: HEM 821 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.296774 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): -18.35400 36.66900 ymin,ymax (A): -32.31200 35.08000 zmin,zma (A): -3.998000 65.75200 x,y,z range (A): 55.02300 67.39200 69.75000 scale (grids/A): 2.296774 object centre (A): 9.157501 1.384001 30.87700 number of atom coordinates read : 4786 total number of charged atoms : 4582 net assigned charge : 3.400030 assigned positive charge : 723.3722 centred at (gu) : 91.04044 92.85646 82.38372 assigned negative charge : -719.9769 centred at (gu) : 90.63393 92.99685 82.63254 start vw surface at 0.2100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 205373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43042 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90597 mr = 147074 m= 22679 mr = 70071 m= 3169 mr = 15780 m= 153 mr = 1834 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 1.600000 number of dielectric boundary points 87163 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 36557 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) : 1.531183 object centre at (A) : 9.157501 1.384001 30.87700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1272870 -0.1531876 midg,1,midg; midg,igrid,midg -8.1397392E-02 -0.1714415 1,midg,midg; igrid,midg,midg -1.9063443E-02 0.1642397 gauss-seidel spectral radius is 0.9991640 estimated iterations to convergence 273 setup time was (sec) 1.960000 now iterating at: 17:15:46 rms-change max change #iterations 10.36781 272.2193 at 10iterations 5.965816 134.6936 at 20iterations 3.388207 74.80549 at 30iterations 1.919451 47.85105 at 40iterations 1.082780 25.68072 at 50iterations 0.6087067 14.48791 at 60iterations 0.3413359 7.576908 at 70iterations 0.1911934 4.642757 at 80iterations 0.1066994 2.191935 at 90iterations 5.9609409E-02 1.196259 at 100iterations 3.3270769E-02 0.6143227 at 110iterations 1.8474804E-02 0.3650780 at 120iterations 1.0302681E-02 0.2024460 at 130iterations 5.7420973E-03 0.1179352 at 140iterations 3.1963978E-03 5.9132576E-02 at 150iterations 1.7814133E-03 3.3439636E-02 at 160iterations 9.9514856E-04 2.0581245E-02 at 170iterations 5.5883476E-04 1.0756016E-02 at 180iterations finished qdiffx linear iterations at : 17:15:58 total time elapsed so far: 13.98000 # loops : 180 mean,max change (kT/e) : 5.5883476E-04 1.0756016E-02 energy calculations done at 13.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.17000 DelPhi exited at 17:15:58 14.167u 0.281s 0:14.92 96.7% 0+0k 0+0io 0pf+0w