Mon Oct 10 18:47:42 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 18:47:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2182 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: 0.6308254 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): -9.604000 46.83000 ymin,ymax (A): 63.05300 118.1320 zmin,zma (A): 47.65600 88.57899 x,y,z range (A): 56.43400 55.07899 40.92300 scale (grids/A): 0.6308254 object centre (A): 18.61300 90.59250 68.11749 number of atom coordinates read : 2182 total number of charged atoms : 2045 net assigned charge : 5.8710575E-06 assigned positive charge : 324.2702 centred at (gu) : 88.70892 90.71794 90.05750 assigned negative charge : -324.2707 centred at (gu) : 88.81695 90.79176 90.15936 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5928 nv = 96 ne = 84 npr = 44081 no. pairs analyzed = 44081 no. exposed pairs = 2819 no. arc points = 19844 no. surface atoms = 949 nbur = 1233 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3206 m= 0 mr = 46 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1958 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7040 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4515301E-09 -7.9348723E-09 midg,1,midg; midg,igrid,midg 4.6714219E-09 -6.6587464E-09 1,midg,midg; igrid,midg,midg 1.0669099E-08 -6.2600898E-09 gauss-seidel spectral radius is 0.9869490 estimated iterations to convergence 72 setup time was (sec) 0.4800000 now iterating at: 18:47:43 rms-change max change #iterations 0.1229216 18.45374 at 10iterations 1.1829513E-02 2.194647 at 20iterations 1.1881895E-03 0.1756363 at 30iterations 1.6481521E-04 2.6611328E-02 at 40iterations 3.4567078E-05 5.9890747E-03 at 50iterations finished qdiffx linear iterations at : 18:47:46 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 3.4567078E-05 5.9890747E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 18:47:46 3.213u 0.155s 0:03.88 86.5% 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 18:47:46 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 = 2182 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: 1.892476 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): -9.604000 46.83000 ymin,ymax (A): 63.05300 118.1320 zmin,zma (A): 47.65600 88.57899 x,y,z range (A): 56.43400 55.07899 40.92300 scale (grids/A): 1.892476 object centre (A): 18.61300 90.59250 68.11749 number of atom coordinates read : 2182 total number of charged atoms : 2045 net assigned charge : 5.8710575E-06 assigned positive charge : 324.2702 centred at (gu) : 86.12636 92.15320 90.17224 assigned negative charge : -324.2707 centred at (gu) : 86.45058 92.37499 90.47784 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19844 grid for indexing accessible points = 1.400000 m= 23934 mr = 43895 m= 3872 mr = 17582 m= 227 mr = 2377 m= 4 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 293 time to turn everything in is 0.4700000 number of dielectric boundary points 27744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 16089 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) : 0.6308254 object centre at (A) : 18.61300 90.59250 68.11749 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2092874E-03 -1.1826421E-03 midg,1,midg; midg,igrid,midg 2.0531520E-02 -1.5479041E-02 1,midg,midg; igrid,midg,midg -3.1107112E-03 -6.6051497E-03 gauss-seidel spectral radius is 0.9985784 estimated iterations to convergence 210 setup time was (sec) 0.7200000 now iterating at: 18:47:47 rms-change max change #iterations 3.778725 172.4548 at 10iterations 1.737746 69.33964 at 20iterations 0.8028464 29.61012 at 30iterations 0.3690925 12.42282 at 40iterations 0.1704176 5.579901 at 50iterations 7.8524217E-02 2.758232 at 60iterations 3.6259625E-02 1.221998 at 70iterations 1.6766911E-02 0.5866413 at 80iterations 7.7416929E-03 0.2662628 at 90iterations 3.5758470E-03 0.1134491 at 100iterations 1.6665824E-03 5.4771423E-02 at 110iterations 7.7614625E-04 2.7671814E-02 at 120iterations finished qdiffx linear iterations at : 18:47:53 total time elapsed so far: 6.620000 # loops : 120 mean,max change (kT/e) : 7.7614625E-04 2.7671814E-02 energy calculations done at 6.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.790000 DelPhi exited at 18:47:54 6.794u 0.168s 0:07.23 96.1% 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 18:47:54 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 = 2182 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: 2.838714 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): -9.604000 46.83000 ymin,ymax (A): 63.05300 118.1320 zmin,zma (A): 47.65600 88.57899 x,y,z range (A): 56.43400 55.07899 40.92300 scale (grids/A): 2.838714 object centre (A): 18.61300 90.59250 68.11749 number of atom coordinates read : 2182 total number of charged atoms : 2045 net assigned charge : 5.8710575E-06 assigned positive charge : 324.2702 centred at (gu) : 84.18940 93.22967 90.25816 assigned negative charge : -324.2707 centred at (gu) : 84.67585 93.56238 90.71677 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 146930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19844 grid for indexing accessible points = 1.400000 m= 76102 mr = 106203 m= 28556 mr = 62093 m= 6990 mr = 22846 m= 991 mr = 5295 m= 60 mr = 651 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 983 time to turn everything in is 1.150000 number of dielectric boundary points 62526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 16359 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) : 1.892476 object centre at (A) : 18.61300 90.59250 68.11749 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0288483E-02 1.0908903E-02 midg,1,midg; midg,igrid,midg 0.4313752 -0.1916812 1,midg,midg; igrid,midg,midg -7.9558633E-02 0.2659445 gauss-seidel spectral radius is 0.9992344 estimated iterations to convergence 285 setup time was (sec) 1.430000 now iterating at: 18:47:55 rms-change max change #iterations 9.033766 324.0668 at 10iterations 5.287626 146.5586 at 20iterations 3.066272 75.43176 at 30iterations 1.763911 38.63886 at 40iterations 1.015818 23.50628 at 50iterations 0.5801401 12.17015 at 60iterations 0.3328203 7.526993 at 70iterations 0.1903498 3.637741 at 80iterations 0.1086865 2.126152 at 90iterations 6.2254470E-02 1.357124 at 100iterations 3.5485346E-02 0.7444706 at 110iterations 2.0213528E-02 0.3707142 at 120iterations 1.1524560E-02 0.2771492 at 130iterations 6.5777060E-03 0.1245751 at 140iterations 3.7528849E-03 7.5570107E-02 at 150iterations 2.1523773E-03 4.2348862E-02 at 160iterations 1.2379928E-03 2.3103237E-02 at 170iterations 7.1512623E-04 1.4793396E-02 at 180iterations finished qdiffx linear iterations at : 18:48:05 total time elapsed so far: 10.76000 # loops : 180 mean,max change (kT/e) : 7.1512623E-04 1.4793396E-02 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.93000 DelPhi exited at 18:48:05 10.936u 0.154s 0:11.55 95.9% 0+0k 0+0io 0pf+0w