Tue Oct 11 06:19:50 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 Tue Oct 11 2011 at 06:19:50 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 = 2064 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: 0.6952582 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): -15.31400 24.98000 ymin,ymax (A): -0.7409999 40.64800 zmin,zma (A): 0.7459999 51.95000 x,y,z range (A): 40.29400 41.38900 51.20400 scale (grids/A): 0.6952582 object centre (A): 4.833000 19.95350 26.34800 number of atom coordinates read : 2064 total number of charged atoms : 1935 net assigned charge : 6.500006 assigned positive charge : 312.9640 centred at (gu) : 90.68832 89.21520 90.22222 assigned negative charge : -306.4642 centred at (gu) : 90.81615 89.10802 90.23126 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6810 nv = 96 ne = 84 npr = 41463 no. pairs analyzed = 41463 no. exposed pairs = 2429 no. arc points = 16923 no. surface atoms = 830 nbur = 1234 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3903 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1709 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7668 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3106898E-08 3.9986986E-08 midg,1,midg; midg,igrid,midg 1.6475840E-09 6.9179904E-08 1,midg,midg; igrid,midg,midg 7.6952645E-08 -7.2859376E-09 gauss-seidel spectral radius is 0.9892178 estimated iterations to convergence 78 setup time was (sec) 0.6900000 now iterating at: 06:19:51 rms-change max change #iterations 0.1844712 25.83821 at 10iterations 2.1908080E-02 3.245816 at 20iterations 2.7912131E-03 0.4488335 at 30iterations 4.3759236E-04 5.9957504E-02 at 40iterations 1.0307851E-04 1.2908936E-02 at 50iterations finished qdiffx linear iterations at : 06:19:55 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 1.0307851E-04 1.2908936E-02 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 06:19:56 4.695u 0.418s 0:05.45 93.5% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 06:19:56 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 = 2064 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: 2.085775 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): -15.31400 24.98000 ymin,ymax (A): -0.7409999 40.64800 zmin,zma (A): 0.7459999 51.95000 x,y,z range (A): 40.29400 41.38900 51.20400 scale (grids/A): 2.085775 object centre (A): 4.833000 19.95350 26.34800 number of atom coordinates read : 2064 total number of charged atoms : 1935 net assigned charge : 6.500006 assigned positive charge : 312.9640 centred at (gu) : 92.06478 87.64555 90.66660 assigned negative charge : -306.4642 centred at (gu) : 92.44870 87.32419 90.69407 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72143 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16923 grid for indexing accessible points = 1.400000 m= 28377 mr = 51342 m= 5271 mr = 21622 m= 475 mr = 3431 m= 12 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 29632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 15372 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) : 0.6952582 object centre at (A) : 4.833000 19.95350 26.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5174476E-02 4.5311160E-02 midg,1,midg; midg,igrid,midg 6.3592284E-03 2.0430705E-02 1,midg,midg; igrid,midg,midg 3.5680290E-02 1.7237777E-03 gauss-seidel spectral radius is 0.9987928 estimated iterations to convergence 228 setup time was (sec) 1.120000 now iterating at: 06:19:57 rms-change max change #iterations 4.425713 206.7893 at 10iterations 2.169483 76.19225 at 20iterations 1.061970 34.23656 at 30iterations 0.5223669 15.98270 at 40iterations 0.2560590 8.533016 at 50iterations 0.1252167 3.750427 at 60iterations 6.1849311E-02 1.927078 at 70iterations 3.0356999E-02 0.9987335 at 80iterations 1.4909470E-02 0.4677391 at 90iterations 7.3567154E-03 0.2694683 at 100iterations 3.6377197E-03 0.1135254 at 110iterations 1.8085390E-03 5.4985046E-02 at 120iterations finished qdiffx linear iterations at : 06:20:07 total time elapsed so far: 10.90000 # loops : 120 mean,max change (kT/e) : 1.8085390E-03 5.4985046E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 06:20:08 11.125u 0.473s 0:12.27 94.4% 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 Tue Oct 11 2011 at 06:20:08 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 = 2064 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: 3.128662 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): -15.31400 24.98000 ymin,ymax (A): -0.7409999 40.64800 zmin,zma (A): 0.7459999 51.95000 x,y,z range (A): 40.29400 41.38900 51.20400 scale (grids/A): 3.128662 object centre (A): 4.833000 19.95350 26.34800 number of atom coordinates read : 2064 total number of charged atoms : 1935 net assigned charge : 6.500006 assigned positive charge : 312.9640 centred at (gu) : 93.09725 86.46847 91.00002 assigned negative charge : -306.4642 centred at (gu) : 93.67310 85.98626 91.04110 start vw surface at 0.1400000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 166320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16923 grid for indexing accessible points = 1.400000 m= 89785 mr = 123677 m= 35357 mr = 74819 m= 9792 mr = 28998 m= 1931 mr = 7564 m= 223 mr = 1396 m= 7 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.320000 number of dielectric boundary points 66813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.480000 number of grid points assigned charge 15480 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) : 2.085775 object centre at (A) : 4.833000 19.95350 26.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3445868 0.2944789 midg,1,midg; midg,igrid,midg 8.4421292E-02 0.1498726 1,midg,midg; igrid,midg,midg 0.3435635 2.5411246E-02 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 2.700000 now iterating at: 06:20:11 rms-change max change #iterations 9.963020 396.4927 at 10iterations 5.847932 126.8858 at 20iterations 3.439896 70.24442 at 30iterations 2.011615 40.79278 at 40iterations 1.177435 24.84389 at 50iterations 0.6884692 16.18469 at 60iterations 0.4012859 7.132183 at 70iterations 0.2338544 4.134794 at 80iterations 0.1364654 2.433541 at 90iterations 7.9599857E-02 1.526716 at 100iterations 4.6444185E-02 0.7867746 at 110iterations 2.7167384E-02 0.5219526 at 120iterations 1.5927253E-02 0.2875290 at 130iterations 9.4554536E-03 0.1603726 at 140iterations 5.6806714E-03 0.1045382 at 150iterations 3.5104714E-03 6.8737745E-02 at 160iterations 2.2537829E-03 4.1538239E-02 at 170iterations 1.5325304E-03 2.9359818E-02 at 180iterations finished qdiffx linear iterations at : 06:20:28 total time elapsed so far: 18.95000 # loops : 180 mean,max change (kT/e) : 1.5325304E-03 2.9359818E-02 energy calculations done at 18.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.17000 DelPhi exited at 06:20:28 19.179u 0.502s 0:20.32 96.8% 0+0k 0+0io 0pf+0w