Sat Oct 8 16:27:48 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 Sat Oct 8 2011 at 16:27:48 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2343 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 0.6423674 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): -7.305000 47.75100 ymin,ymax (A): -17.47400 29.91700 zmin,zma (A): -19.12900 36.29100 x,y,z range (A): 55.05600 47.39100 55.42000 scale (grids/A): 0.6423674 object centre (A): 20.22300 6.221499 8.581000 number of atom coordinates read : 2343 total number of charged atoms : 2249 net assigned charge : 5.900012 assigned positive charge : 348.7950 centred at (gu) : 91.03790 89.04321 90.24432 assigned negative charge : -342.8958 centred at (gu) : 91.13760 89.16326 90.23832 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6443 nv = 96 ne = 84 npr = 48251 no. pairs analyzed = 48251 no. exposed pairs = 2856 no. arc points = 19843 no. surface atoms = 979 nbur = 1364 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 352 mr = 3588 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1973 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0989633E-09 1.0339253E-08 midg,1,midg; midg,igrid,midg 2.7208165E-08 -3.3067404E-09 1,midg,midg; igrid,midg,midg 1.6064046E-08 -2.5098406E-09 gauss-seidel spectral radius is 0.9874189 estimated iterations to convergence 73 setup time was (sec) 0.7000000 now iterating at: 16:27:49 rms-change max change #iterations 0.1335403 20.45596 at 10iterations 1.3824034E-02 1.972536 at 20iterations 1.4750754E-03 0.2224121 at 30iterations 1.9598514E-04 3.3016205E-02 at 40iterations 3.9160128E-05 6.1987638E-03 at 50iterations finished qdiffx linear iterations at : 16:27:53 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 3.9160128E-05 6.1987638E-03 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 16:27:53 4.628u 0.417s 0:05.34 94.1% 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 Sat Oct 8 2011 at 16:27:53 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2343 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 1.927102 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): -7.305000 47.75100 ymin,ymax (A): -17.47400 29.91700 zmin,zma (A): -19.12900 36.29100 x,y,z range (A): 55.05600 47.39100 55.42000 scale (grids/A): 1.927102 object centre (A): 20.22300 6.221499 8.581000 number of atom coordinates read : 2343 total number of charged atoms : 2249 net assigned charge : 5.900012 assigned positive charge : 348.7950 centred at (gu) : 93.11339 87.12905 90.73254 assigned negative charge : -342.8958 centred at (gu) : 93.41264 87.48985 90.71497 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19843 grid for indexing accessible points = 1.400000 m= 25008 mr = 48350 m= 4278 mr = 18488 m= 263 mr = 2768 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 28999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 17719 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) : 0.6423674 object centre at (A) : 20.22300 6.221499 8.581000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6160911E-02 2.6953429E-02 midg,1,midg; midg,igrid,midg 2.2903193E-02 -6.1028791E-03 1,midg,midg; igrid,midg,midg 3.6052670E-02 -4.4154432E-02 gauss-seidel spectral radius is 0.9986337 estimated iterations to convergence 214 setup time was (sec) 1.050000 now iterating at: 16:27:55 rms-change max change #iterations 4.064630 175.8534 at 10iterations 1.895069 71.31497 at 20iterations 0.8882115 29.78573 at 30iterations 0.4152562 12.78924 at 40iterations 0.1954821 6.129836 at 50iterations 9.0992831E-02 2.825821 at 60iterations 4.2859256E-02 1.366627 at 70iterations 2.0119492E-02 0.6703440 at 80iterations 9.4175013E-03 0.3211422 at 90iterations 4.4358079E-03 0.1545563 at 100iterations 2.0878396E-03 6.9160461E-02 at 110iterations 9.8696968E-04 3.0369163E-02 at 120iterations finished qdiffx linear iterations at : 16:28:04 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 9.8696968E-04 3.0369163E-02 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.49000 DelPhi exited at 16:28:05 10.496u 0.463s 0:11.34 96.5% 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 Sat Oct 8 2011 at 16:28:05 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2343 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 2.890653 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): -7.305000 47.75100 ymin,ymax (A): -17.47400 29.91700 zmin,zma (A): -19.12900 36.29100 x,y,z range (A): 55.05600 47.39100 55.42000 scale (grids/A): 2.890653 object centre (A): 20.22300 6.221499 8.581000 number of atom coordinates read : 2343 total number of charged atoms : 2249 net assigned charge : 5.900012 assigned positive charge : 348.7950 centred at (gu) : 94.66995 85.69356 91.09872 assigned negative charge : -342.8958 centred at (gu) : 95.11888 86.23483 91.07246 start vw surface at 0.1600000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 160360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19843 grid for indexing accessible points = 1.400000 m= 80238 mr = 117478 m= 29808 mr = 65763 m= 7949 mr = 24114 m= 1149 mr = 6074 m= 71 mr = 729 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.900000 number of dielectric boundary points 65387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 17991 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) : 1.927102 object centre at (A) : 20.22300 6.221499 8.581000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2820034 0.2895412 midg,1,midg; midg,igrid,midg 0.1766989 -0.1049517 1,midg,midg; igrid,midg,midg 0.7117991 -0.6381423 gauss-seidel spectral radius is 0.9992505 estimated iterations to convergence 288 setup time was (sec) 2.250000 now iterating at: 16:28:07 rms-change max change #iterations 9.602019 418.4486 at 10iterations 5.603390 138.2030 at 20iterations 3.260438 73.74133 at 30iterations 1.888738 42.74579 at 40iterations 1.094279 22.05818 at 50iterations 0.6315081 13.40456 at 60iterations 0.3640375 6.620548 at 70iterations 0.2096192 3.970198 at 80iterations 0.1206572 2.316982 at 90iterations 6.9416843E-02 1.376787 at 100iterations 3.9765351E-02 0.7489939 at 110iterations 2.2863092E-02 0.4397163 at 120iterations 1.3136433E-02 0.2468567 at 130iterations 7.5416476E-03 0.1495552 at 140iterations 4.3446994E-03 7.8449249E-02 at 150iterations 2.5032859E-03 5.3443909E-02 at 160iterations 1.4547375E-03 2.6549339E-02 at 170iterations 8.4986677E-04 1.5296936E-02 at 180iterations finished qdiffx linear iterations at : 16:28:23 total time elapsed so far: 17.79000 # loops : 180 mean,max change (kT/e) : 8.4986677E-04 1.5296936E-02 energy calculations done at 17.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.01000 DelPhi exited at 16:28:23 18.017u 0.462s 0:18.77 98.4% 0+0k 0+0io 0pf+0w