Mon Oct 10 14:01:47 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 14:01:47 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 = 2143 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6227151 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): 69.05700 126.2260 ymin,ymax (A): -7.668000 37.09600 zmin,zma (A): 3.469000 52.12200 x,y,z range (A): 57.16900 44.76400 48.65300 scale (grids/A): 0.6227151 object centre (A): 97.64149 14.71400 27.79550 number of atom coordinates read : 2143 total number of charged atoms : 2076 net assigned charge : 0.5000287 assigned positive charge : 319.6157 centred at (gu) : 90.14930 89.04490 89.01192 assigned negative charge : -319.1164 centred at (gu) : 90.25222 89.09904 89.12689 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5569 nv = 96 ne = 84 npr = 41896 no. pairs analyzed = 41896 no. exposed pairs = 3102 no. arc points = 20895 no. surface atoms = 1033 nbur = 1110 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 2750 m= 0 mr = 43 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2027 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6861 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7951744E-09 -5.2382645E-09 midg,1,midg; midg,igrid,midg 4.3614548E-09 -2.3176863E-09 1,midg,midg; igrid,midg,midg 6.1451244E-09 -6.0004419E-09 gauss-seidel spectral radius is 0.9866133 estimated iterations to convergence 71 setup time was (sec) 0.4700000 now iterating at: 14:01:48 rms-change max change #iterations 0.1161162 19.33586 at 10iterations 1.0713135E-02 1.723694 at 20iterations 9.7696122E-04 0.1949959 at 30iterations 9.0980109E-05 1.3885498E-02 at 40iterations 8.4936564E-06 1.6708374E-03 at 50iterations finished qdiffx linear iterations at : 14:01:50 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 8.4936564E-06 1.6708374E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 14:01:51 3.250u 0.141s 0:03.95 85.8% 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 14:01:51 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 = 2143 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: 1.868145 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): 69.05700 126.2260 ymin,ymax (A): -7.668000 37.09600 zmin,zma (A): 3.469000 52.12200 x,y,z range (A): 57.16900 44.76400 48.65300 scale (grids/A): 1.868145 object centre (A): 97.64149 14.71400 27.79550 number of atom coordinates read : 2143 total number of charged atoms : 2076 net assigned charge : 0.5000287 assigned positive charge : 319.6157 centred at (gu) : 90.44765 87.13452 87.03540 assigned negative charge : -319.1164 centred at (gu) : 90.75676 87.29719 87.38094 start vw surface at 0.2100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 59500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20895 grid for indexing accessible points = 1.400000 m= 20776 mr = 38444 m= 3597 mr = 14497 m= 224 mr = 2274 m= 2 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 28798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 16291 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) : 0.6227151 object centre at (A) : 97.64149 14.71400 27.79550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0360606E-02 4.6327836E-03 midg,1,midg; midg,igrid,midg 6.3655181E-03 -2.8052619E-03 1,midg,midg; igrid,midg,midg -1.0827065E-02 -1.6695080E-02 gauss-seidel spectral radius is 0.9985465 estimated iterations to convergence 208 setup time was (sec) 0.8000000 now iterating at: 14:01:52 rms-change max change #iterations 3.660228 182.0037 at 10iterations 1.667199 65.08978 at 20iterations 0.7621358 26.27537 at 30iterations 0.3486124 13.63404 at 40iterations 0.1593841 5.597534 at 50iterations 7.2991431E-02 2.684316 at 60iterations 3.3181176E-02 1.097364 at 70iterations 1.5191136E-02 0.5132446 at 80iterations 6.9466024E-03 0.2807682 at 90iterations 3.1741143E-03 0.1170101 at 100iterations 1.4502079E-03 5.9768677E-02 at 110iterations 6.6377519E-04 2.3198605E-02 at 120iterations finished qdiffx linear iterations at : 14:01:58 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 6.6377519E-04 2.3198605E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 14:01:59 6.930u 0.179s 0:07.92 89.6% 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 14:01:59 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 = 2143 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: 2.802218 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): 69.05700 126.2260 ymin,ymax (A): -7.668000 37.09600 zmin,zma (A): 3.469000 52.12200 x,y,z range (A): 57.16900 44.76400 48.65300 scale (grids/A): 2.802218 object centre (A): 97.64149 14.71400 27.79550 number of atom coordinates read : 2143 total number of charged atoms : 2076 net assigned charge : 0.5000287 assigned positive charge : 319.6157 centred at (gu) : 90.67155 85.70177 85.55312 assigned negative charge : -319.1164 centred at (gu) : 91.13518 85.94583 86.07143 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 137424 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20895 grid for indexing accessible points = 1.400000 m= 66163 mr = 94051 m= 25004 mr = 51846 m= 6484 mr = 19648 m= 1049 mr = 4910 m= 62 mr = 740 m= 0 mr = 13 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 64978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 16607 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) : 1.868145 object centre at (A) : 97.64149 14.71400 27.79550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3318758 7.1342438E-02 midg,1,midg; midg,igrid,midg 8.9887276E-02 -1.7841011E-02 1,midg,midg; igrid,midg,midg -0.3540938 -0.1762972 gauss-seidel spectral radius is 0.9992357 estimated iterations to convergence 286 setup time was (sec) 1.360000 now iterating at: 14:02:01 rms-change max change #iterations 8.699563 316.9473 at 10iterations 5.029787 122.6025 at 20iterations 2.891432 78.78525 at 30iterations 1.654706 37.35643 at 40iterations 0.9478995 22.10198 at 50iterations 0.5412799 10.80182 at 60iterations 0.3081761 6.413952 at 70iterations 0.1759598 3.465366 at 80iterations 0.1001038 2.350681 at 90iterations 5.6959365E-02 1.076683 at 100iterations 3.2512065E-02 0.6891294 at 110iterations 1.8472139E-02 0.3673038 at 120iterations 1.0498972E-02 0.2109318 at 130iterations 5.9789876E-03 0.1227856 at 140iterations 3.4082246E-03 6.9181442E-02 at 150iterations 1.9393767E-03 3.8124084E-02 at 160iterations 1.1019215E-03 2.1821380E-02 at 170iterations 6.2581559E-04 1.2609482E-02 at 180iterations finished qdiffx linear iterations at : 14:02:11 total time elapsed so far: 11.28000 # loops : 180 mean,max change (kT/e) : 6.2581559E-04 1.2609482E-02 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 14:02:12 11.465u 0.221s 0:12.93 90.3% 0+0k 0+0io 0pf+0w