Sat Oct 8 16:27:13 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 Sat Oct 8 2011 at 16:27:13 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 = 2343 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 : 6.000011 assigned positive charge : 346.0951 centred at (gu) : 91.00526 89.05235 90.26626 assigned negative charge : -340.0958 centred at (gu) : 91.10465 89.17002 90.25882 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 = 0.1500000 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 = 0.2000000 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 0.4900000 number of grid points assigned charge 7870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0663671E-09 1.0710925E-08 midg,1,midg; midg,igrid,midg 2.6902857E-08 -2.8809946E-09 1,midg,midg; igrid,midg,midg 1.6204652E-08 -2.1436335E-09 gauss-seidel spectral radius is 0.9874189 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 16:27:14 rms-change max change #iterations 0.1297847 18.68153 at 10iterations 1.3500200E-02 2.003172 at 20iterations 1.4334595E-03 0.2121964 at 30iterations 1.8590043E-04 3.0818939E-02 at 40iterations 3.6187826E-05 5.7241917E-03 at 50iterations finished qdiffx linear iterations at : 16:27:17 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 3.6187826E-05 5.7241917E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 16:27:18 4.557u 0.378s 0:05.24 93.8% 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 Sat Oct 8 2011 at 16:27:18 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 = 2343 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 : 6.000011 assigned positive charge : 346.0951 centred at (gu) : 93.01549 87.15656 90.79839 assigned negative charge : -340.0958 centred at (gu) : 93.31380 87.51011 90.77644 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 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 = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 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 0.8800000 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 2.5442058E-02 2.6700454E-02 midg,1,midg; midg,igrid,midg 2.2350941E-02 -5.4479241E-03 1,midg,midg; igrid,midg,midg 3.6422234E-02 -4.2097084E-02 gauss-seidel spectral radius is 0.9986337 estimated iterations to convergence 214 setup time was (sec) 1.070000 now iterating at: 16:27:19 rms-change max change #iterations 4.017550 175.8534 at 10iterations 1.872262 71.30141 at 20iterations 0.8774877 30.11281 at 30iterations 0.4103776 12.71428 at 40iterations 0.1932019 6.245879 at 50iterations 8.9991182E-02 2.781940 at 60iterations 4.2350993E-02 1.340088 at 70iterations 1.9884404E-02 0.6660290 at 80iterations 9.3026673E-03 0.3138828 at 90iterations 4.3838681E-03 0.1544304 at 100iterations 2.0588818E-03 6.9004059E-02 at 110iterations 9.7317074E-04 3.0427933E-02 at 120iterations finished qdiffx linear iterations at : 16:27:28 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 9.7317074E-04 3.0427933E-02 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.41000 DelPhi exited at 16:27:29 10.413u 0.439s 0:11.20 96.7% 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 Sat Oct 8 2011 at 16:27:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2343 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 : 6.000011 assigned positive charge : 346.0951 centred at (gu) : 94.52312 85.73479 91.19751 assigned negative charge : -340.0958 centred at (gu) : 94.97059 86.26522 91.16464 start vw surface at 0.1500000 fill in re-entrant regions at 0.6200000 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 = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 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 2.030000 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 0.2755415 0.2863546 midg,1,midg; midg,igrid,midg 0.1703866 -9.7688161E-02 1,midg,midg; igrid,midg,midg 0.7158718 -0.6090357 gauss-seidel spectral radius is 0.9992505 estimated iterations to convergence 288 setup time was (sec) 2.230000 now iterating at: 16:27:32 rms-change max change #iterations 9.508283 418.4473 at 10iterations 5.550939 138.0471 at 20iterations 3.229799 73.71659 at 30iterations 1.871690 41.27507 at 40iterations 1.084820 21.88632 at 50iterations 0.6261588 12.82920 at 60iterations 0.3611174 6.518932 at 70iterations 0.2079307 3.939430 at 80iterations 0.1197175 2.275246 at 90iterations 6.8878531E-02 1.354019 at 100iterations 3.9448675E-02 0.7509465 at 110iterations 2.2680020E-02 0.4363441 at 120iterations 1.3026218E-02 0.2422562 at 130iterations 7.4771862E-03 0.1496487 at 140iterations 4.3054228E-03 8.0102921E-02 at 150iterations 2.4773115E-03 5.2957535E-02 at 160iterations 1.4358439E-03 2.6550770E-02 at 170iterations 8.3599857E-04 1.5068293E-02 at 180iterations finished qdiffx linear iterations at : 16:27:47 total time elapsed so far: 17.35000 # loops : 180 mean,max change (kT/e) : 8.3599857E-04 1.5068293E-02 energy calculations done at 17.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.57000 DelPhi exited at 16:27:48 17.571u 0.472s 0:18.41 97.9% 0+0k 0+0io 0pf+0w