Sun Oct 9 16:03:19 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 Sun Oct 9 2011 at 16:03:19 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 = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6349320 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): -15.53100 37.54000 ymin,ymax (A): 55.09700 108.4050 zmin,zma (A): -5.196000 50.87300 x,y,z range (A): 53.07100 53.30800 56.06900 scale (grids/A): 0.6349320 object centre (A): 11.00450 81.75100 22.83850 number of atom coordinates read : 3056 total number of charged atoms : 2912 net assigned charge : -4.499983 assigned positive charge : 450.4791 centred at (gu) : 90.17371 88.68114 91.39445 assigned negative charge : -454.9805 centred at (gu) : 90.21051 88.54368 91.43011 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8133 nv = 96 ne = 84 npr = 63344 no. pairs analyzed = 63344 no. exposed pairs = 3713 no. arc points = 25772 no. surface atoms = 1261 nbur = 1795 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 470 mr = 4464 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2573 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10023 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7994806E-10 -1.2879719E-08 midg,1,midg; midg,igrid,midg -2.9142415E-08 7.9873965E-09 1,midg,midg; igrid,midg,midg -9.3999186E-10 -1.0050140E-08 gauss-seidel spectral radius is 0.9871889 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 16:03:20 rms-change max change #iterations 0.1561837 29.78642 at 10iterations 1.5104027E-02 2.065830 at 20iterations 1.5152353E-03 0.2110411 at 30iterations 1.6019476E-04 2.1766663E-02 at 40iterations 2.1340224E-05 2.7997494E-03 at 50iterations finished qdiffx linear iterations at : 16:03:22 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 2.1340224E-05 2.7997494E-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) 3.200000 DelPhi exited at 16:03:23 3.205u 0.154s 0:03.68 91.0% 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 16:03:23 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 = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.904796 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): -15.53100 37.54000 ymin,ymax (A): 55.09700 108.4050 zmin,zma (A): -5.196000 50.87300 x,y,z range (A): 53.07100 53.30800 56.06900 scale (grids/A): 1.904796 object centre (A): 11.00450 81.75100 22.83850 number of atom coordinates read : 3056 total number of charged atoms : 2912 net assigned charge : -4.499983 assigned positive charge : 450.4791 centred at (gu) : 90.52014 86.04250 94.18265 assigned negative charge : -454.9805 centred at (gu) : 90.63173 85.63097 94.29009 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25772 grid for indexing accessible points = 1.400000 m= 32174 mr = 61887 m= 5633 mr = 23380 m= 372 mr = 3539 m= 5 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 440 time to turn everything in is 0.6200000 number of dielectric boundary points 37481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22969 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) : 0.6349320 object centre at (A) : 11.00450 81.75100 22.83850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8946247E-02 1.2108291E-02 midg,1,midg; midg,igrid,midg -3.4215439E-02 -8.0208583E-03 1,midg,midg; igrid,midg,midg -4.0222999E-02 -3.2191724E-02 gauss-seidel spectral radius is 0.9986739 estimated iterations to convergence 218 setup time was (sec) 0.8900000 now iterating at: 16:03:24 rms-change max change #iterations 4.599974 165.4207 at 10iterations 2.175528 74.89798 at 20iterations 1.028936 33.37690 at 30iterations 0.4861920 14.14534 at 40iterations 0.2297339 6.709427 at 50iterations 0.1088083 3.048970 at 60iterations 5.1299870E-02 1.468147 at 70iterations 2.4338996E-02 0.6851630 at 80iterations 1.1544794E-02 0.3274612 at 90iterations 5.4784445E-03 0.1679206 at 100iterations 2.5870304E-03 7.3474884E-02 at 110iterations 1.2287971E-03 3.6315918E-02 at 120iterations finished qdiffx linear iterations at : 16:03:30 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 1.2287971E-03 3.6315918E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 16:03:31 7.363u 0.202s 0:08.13 92.9% 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 16:03:31 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 = 3056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.857194 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): -15.53100 37.54000 ymin,ymax (A): 55.09700 108.4050 zmin,zma (A): -5.196000 50.87300 x,y,z range (A): 53.07100 53.30800 56.06900 scale (grids/A): 2.857194 object centre (A): 11.00450 81.75100 22.83850 number of atom coordinates read : 3056 total number of charged atoms : 2912 net assigned charge : -4.499983 assigned positive charge : 450.4791 centred at (gu) : 90.77996 84.06342 96.27374 assigned negative charge : -454.9805 centred at (gu) : 90.94746 83.44658 96.43518 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 204569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25772 grid for indexing accessible points = 1.400000 m= 102765 mr = 150287 m= 38928 mr = 83382 m= 10021 mr = 31024 m= 1477 mr = 7457 m= 93 mr = 1015 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1531 time to turn everything in is 1.530000 number of dielectric boundary points 84650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 23295 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) : 1.904796 object centre at (A) : 11.00450 81.75100 22.83850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3688046 0.2501815 midg,1,midg; midg,igrid,midg -0.3605930 -0.2447589 1,midg,midg; igrid,midg,midg -0.5088903 -0.3526271 gauss-seidel spectral radius is 0.9992781 estimated iterations to convergence 294 setup time was (sec) 1.820000 now iterating at: 16:03:33 rms-change max change #iterations 10.92278 433.3276 at 10iterations 6.444749 136.5457 at 20iterations 3.774420 74.29249 at 30iterations 2.212242 41.28512 at 40iterations 1.291681 24.21310 at 50iterations 0.7521941 15.28415 at 60iterations 0.4374502 7.951753 at 70iterations 0.2546421 4.424775 at 80iterations 0.1474825 2.638672 at 90iterations 8.5854381E-02 1.566139 at 100iterations 4.9730595E-02 0.8503542 at 110iterations 2.8894797E-02 0.5068831 at 120iterations 1.6757548E-02 0.2752295 at 130iterations 9.7076157E-03 0.1857333 at 140iterations 5.6321514E-03 9.3259811E-02 at 150iterations 3.2720829E-03 6.2494278E-02 at 160iterations 1.8990390E-03 3.1883240E-02 at 170iterations 1.1047277E-03 1.9121647E-02 at 180iterations finished qdiffx linear iterations at : 16:03:42 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 1.1047277E-03 1.9121647E-02 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 16:03:43 11.722u 0.254s 0:12.34 97.0% 0+0k 0+0io 0pf+0w