Sun Oct 9 10:19:24 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 10:19:24 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 0.6687706 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): -1.751000 48.10600 ymin,ymax (A): -26.71700 26.46100 zmin,zma (A): -5.647000 47.58500 x,y,z range (A): 49.85700 53.17800 53.23200 scale (grids/A): 0.6687706 object centre (A): 23.17750 -0.1279993 20.96900 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.514014 assigned positive charge : 322.6026 centred at (gu) : 90.70085 92.35976 91.27701 assigned negative charge : -320.0893 centred at (gu) : 90.74314 92.21007 91.27028 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6889 nv = 96 ne = 84 npr = 44125 no. pairs analyzed = 44125 no. exposed pairs = 2980 no. arc points = 21116 no. surface atoms = 991 nbur = 1219 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3607 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3100000 number of dielectric boundary points 3620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1963 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7743 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6321289E-09 1.1163930E-08 midg,1,midg; midg,igrid,midg -1.4253621E-08 6.0896454E-08 1,midg,midg; igrid,midg,midg 1.3700986E-08 -1.5888243E-09 gauss-seidel spectral radius is 0.9883853 estimated iterations to convergence 76 setup time was (sec) 0.5800000 now iterating at: 10:19:25 rms-change max change #iterations 0.1620461 22.13336 at 10iterations 1.7470460E-02 2.928596 at 20iterations 1.8874543E-03 0.2838860 at 30iterations 2.0743125E-04 2.9930115E-02 at 40iterations 2.2907319E-05 3.6544800E-03 at 50iterations finished qdiffx linear iterations at : 10:19:28 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 2.2907319E-05 3.6544800E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 10:19:29 4.038u 0.249s 0:04.58 93.2% 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 10:19:29 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 2.006312 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): -1.751000 48.10600 ymin,ymax (A): -26.71700 26.46100 zmin,zma (A): -5.647000 47.58500 x,y,z range (A): 49.85700 53.17800 53.23200 scale (grids/A): 2.006312 object centre (A): 23.17750 -0.1279993 20.96900 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.514014 assigned positive charge : 322.6026 centred at (gu) : 92.10238 97.07896 93.83089 assigned negative charge : -320.0893 centred at (gu) : 92.22955 96.63038 93.81107 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21116 grid for indexing accessible points = 1.400000 m= 26539 mr = 48878 m= 4888 mr = 19293 m= 392 mr = 3258 m= 5 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 0.6700000 number of dielectric boundary points 33360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 16399 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) : 0.6687706 object centre at (A) : 23.17750 -0.1279993 20.96900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6969400E-02 5.5905499E-02 midg,1,midg; midg,igrid,midg -1.9014636E-03 6.3817129E-02 1,midg,midg; igrid,midg,midg -1.6638203E-02 -3.0710910E-02 gauss-seidel spectral radius is 0.9987333 estimated iterations to convergence 223 setup time was (sec) 0.9700000 now iterating at: 10:19:30 rms-change max change #iterations 4.252020 180.1289 at 10iterations 2.049823 72.00149 at 20iterations 0.9900895 31.78697 at 30iterations 0.4751205 14.15869 at 40iterations 0.2300376 7.835172 at 50iterations 0.1106825 3.335804 at 60iterations 5.3441301E-02 1.852355 at 70iterations 2.5741868E-02 0.8274231 at 80iterations 1.2425947E-02 0.4058714 at 90iterations 5.9679300E-03 0.1879749 at 100iterations 2.8675930E-03 9.3501091E-02 at 110iterations 1.3811531E-03 4.3662071E-02 at 120iterations finished qdiffx linear iterations at : 10:19:38 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 1.3811531E-03 4.3662071E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 10:19:39 9.456u 0.290s 0:10.00 97.4% 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 Sun Oct 9 2011 at 10:19:39 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 3.009468 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): -1.751000 48.10600 ymin,ymax (A): -26.71700 26.46100 zmin,zma (A): -5.647000 47.58500 x,y,z range (A): 49.85700 53.17800 53.23200 scale (grids/A): 3.009468 object centre (A): 23.17750 -0.1279993 20.96900 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.514014 assigned positive charge : 322.6026 centred at (gu) : 93.15349 100.6185 95.74625 assigned negative charge : -320.0893 centred at (gu) : 93.34442 99.94551 95.71652 start vw surface at 0.1500000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 168849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21116 grid for indexing accessible points = 1.400000 m= 83722 mr = 118747 m= 32411 mr = 67362 m= 9144 mr = 26073 m= 1758 mr = 7122 m= 185 mr = 1385 m= 4 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 2561 time to turn everything in is 1.710000 number of dielectric boundary points 75282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 16584 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) : 2.006312 object centre at (A) : 23.17750 -0.1279993 20.96900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1000640 0.7050783 midg,1,midg; midg,igrid,midg -4.3343671E-02 0.4747969 1,midg,midg; igrid,midg,midg -0.2201360 -0.3619969 gauss-seidel spectral radius is 0.9992893 estimated iterations to convergence 296 setup time was (sec) 2.040000 now iterating at: 10:19:41 rms-change max change #iterations 9.736490 415.9598 at 10iterations 5.703753 116.4219 at 20iterations 3.331183 71.17210 at 30iterations 1.951961 40.54245 at 40iterations 1.135325 21.37310 at 50iterations 0.6615073 13.89710 at 60iterations 0.3860546 7.633879 at 70iterations 0.2247165 3.808681 at 80iterations 0.1305565 2.399563 at 90iterations 7.5987846E-02 1.532920 at 100iterations 4.4053700E-02 0.7728832 at 110iterations 2.5667500E-02 0.4831375 at 120iterations 1.4888212E-02 0.2693272 at 130iterations 8.6480221E-03 0.1517677 at 140iterations 5.0210934E-03 9.0923309E-02 at 150iterations 2.9121398E-03 5.3486586E-02 at 160iterations 1.6941176E-03 3.0551910E-02 at 170iterations 9.8495628E-04 1.8634796E-02 at 180iterations finished qdiffx linear iterations at : 10:19:55 total time elapsed so far: 15.76000 # loops : 180 mean,max change (kT/e) : 9.8495628E-04 1.8634796E-02 energy calculations done at 15.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.94000 DelPhi exited at 10:19:55 15.943u 0.311s 0:16.55 98.1% 0+0k 0+0io 0pf+0w