Tue Oct 11 03:18:36 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 Tue Oct 11 2011 at 03:18:36 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 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: 0.5498495 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): 19.88000 84.62500 ymin,ymax (A): 82.03699 136.3790 zmin,zma (A): 3.729000 52.84800 x,y,z range (A): 64.74500 54.34200 49.11900 scale (grids/A): 0.5498495 object centre (A): 52.25250 109.2080 28.28850 number of atom coordinates read : 3222 total number of charged atoms : 3075 net assigned charge : -9.499990 assigned positive charge : 481.6824 centred at (gu) : 90.15134 89.62641 89.77630 assigned negative charge : -491.1836 centred at (gu) : 90.22752 89.42702 89.92288 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6514 nv = 96 ne = 84 npr = 62447 no. pairs analyzed = 62447 no. exposed pairs = 4376 no. arc points = 30929 no. surface atoms = 1448 nbur = 1774 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 277 mr = 3291 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3700000 number of dielectric boundary points 3487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3148 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8481 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7404492E-10 -1.8419282E-09 midg,1,midg; midg,igrid,midg -2.6478058E-09 8.8092900E-10 1,midg,midg; igrid,midg,midg -3.9453715E-11 -1.3822685E-09 gauss-seidel spectral radius is 0.9829726 estimated iterations to convergence 63 setup time was (sec) 0.7000000 now iterating at: 03:18:37 rms-change max change #iterations 8.0756001E-02 16.35113 at 10iterations 5.7101301E-03 0.8612366 at 20iterations 6.3492719E-04 0.1557465 at 30iterations 1.6238373E-04 4.8225403E-02 at 40iterations 5.0347397E-05 1.5106201E-02 at 50iterations finished qdiffx linear iterations at : 03:18:41 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 5.0347397E-05 1.5106201E-02 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.350000 DelPhi exited at 03:18:42 5.350u 0.424s 0:06.13 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 Tue Oct 11 2011 at 03:18:42 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 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: 1.649548 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): 19.88000 84.62500 ymin,ymax (A): 82.03699 136.3790 zmin,zma (A): 3.729000 52.84800 x,y,z range (A): 64.74500 54.34200 49.11900 scale (grids/A): 1.649548 object centre (A): 52.25250 109.2080 28.28850 number of atom coordinates read : 3222 total number of charged atoms : 3075 net assigned charge : -9.499990 assigned positive charge : 481.6824 centred at (gu) : 90.45325 88.87805 89.32784 assigned negative charge : -491.1836 centred at (gu) : 90.68172 88.28046 89.76796 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72174 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30929 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23339 mr = 48278 m= 2730 mr = 16197 m= 77 mr = 1389 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 778 time to turn everything in is 0.6100000 number of dielectric boundary points 32454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 322 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 23593 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) : 0.5498495 object centre at (A) : 52.25250 109.2080 28.28850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4317050E-05 -1.0935990E-02 midg,1,midg; midg,igrid,midg -3.1589385E-02 3.4697005E-03 1,midg,midg; igrid,midg,midg 5.7025575E-03 -1.5625013E-02 gauss-seidel spectral radius is 0.9982623 estimated iterations to convergence 190 setup time was (sec) 0.9400000 now iterating at: 03:18:43 rms-change max change #iterations 3.595299 195.9928 at 10iterations 1.513746 61.79923 at 20iterations 0.6429453 23.92037 at 30iterations 0.2723266 9.450941 at 40iterations 0.1156437 3.841000 at 50iterations 4.9213126E-02 1.677287 at 60iterations 2.0893486E-02 0.7419586 at 70iterations 8.9193573E-03 0.3168335 at 80iterations 3.8280725E-03 0.1312408 at 90iterations 1.6564983E-03 5.6529999E-02 at 100iterations 7.3618192E-04 2.7378082E-02 at 110iterations 3.4401988E-04 1.5030146E-02 at 120iterations finished qdiffx linear iterations at : 03:18:54 total time elapsed so far: 12.16000 # loops : 120 mean,max change (kT/e) : 3.4401988E-04 1.5030146E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 03:18:55 12.322u 0.503s 0:13.13 97.6% 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 03:18:55 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3222 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.474323 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): 19.88000 84.62500 ymin,ymax (A): 82.03699 136.3790 zmin,zma (A): 3.729000 52.84800 x,y,z range (A): 64.74500 54.34200 49.11900 scale (grids/A): 2.474323 object centre (A): 52.25250 109.2080 28.28850 number of atom coordinates read : 3222 total number of charged atoms : 3075 net assigned charge : -9.499990 assigned positive charge : 481.6824 centred at (gu) : 90.67978 88.31713 88.99133 assigned negative charge : -491.1836 centred at (gu) : 91.02245 87.42059 89.65178 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30929 grid for indexing accessible points = 1.400000 m= 79338 mr = 118665 m= 24593 mr = 62460 m= 4369 mr = 18754 m= 309 mr = 2929 m= 6 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 2458 time to turn everything in is 1.500000 number of dielectric boundary points 73377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 24576 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) : 1.649548 object centre at (A) : 52.25250 109.2080 28.28850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5540721E-03 -0.1421806 midg,1,midg; midg,igrid,midg -0.4507976 4.1258469E-02 1,midg,midg; igrid,midg,midg 0.1427580 -0.1394930 gauss-seidel spectral radius is 0.9991747 estimated iterations to convergence 275 setup time was (sec) 1.870000 now iterating at: 03:18:57 rms-change max change #iterations 9.262889 411.4694 at 10iterations 5.271518 120.8544 at 20iterations 2.970707 70.45068 at 30iterations 1.676700 38.31824 at 40iterations 0.9369455 18.89428 at 50iterations 0.5241193 11.46122 at 60iterations 0.2930097 5.759594 at 70iterations 0.1634788 3.496028 at 80iterations 9.1087632E-02 1.698143 at 90iterations 5.0783567E-02 1.086773 at 100iterations 2.8238337E-02 0.5685377 at 110iterations 1.5714362E-02 0.3118248 at 120iterations 8.7944102E-03 0.1646600 at 130iterations 4.8898254E-03 9.1264725E-02 at 140iterations 2.7405433E-03 5.6182861E-02 at 150iterations 1.5334500E-03 3.6954880E-02 at 160iterations 8.6505600E-04 1.9111633E-02 at 170iterations 4.9386919E-04 1.1293411E-02 at 180iterations finished qdiffx linear iterations at : 03:19:16 total time elapsed so far: 20.24000 # loops : 180 mean,max change (kT/e) : 4.9386919E-04 1.1293411E-02 energy calculations done at 20.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.41000 DelPhi exited at 03:19:16 20.410u 0.519s 0:21.25 98.4% 0+0k 0+0io 0pf+0w