Sun Oct 9 23:45:39 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 23:45:39 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 = 3141 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: 0.5909695 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): -30.12600 30.11400 ymin,ymax (A): 7.942000 61.88600 zmin,zma (A): 25.04600 76.19600 x,y,z range (A): 60.24000 53.94400 51.15000 scale (grids/A): 0.5909695 object centre (A): -5.9995651E-03 34.91400 50.62100 number of atom coordinates read : 3141 total number of charged atoms : 2996 net assigned charge : 0.5000069 assigned positive charge : 472.9330 centred at (gu) : 90.00533 89.01875 89.25341 assigned negative charge : -472.4342 centred at (gu) : 90.03022 89.04127 89.36965 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7296 nv = 96 ne = 84 npr = 62765 no. pairs analyzed = 62765 no. exposed pairs = 4114 no. arc points = 29023 no. surface atoms = 1374 nbur = 1767 mkacc time = 0.1100000 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 = 1.456000 m= 309 mr = 3813 m= 0 mr = 8 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2897 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9184 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7087148E-09 -3.2045862E-09 midg,1,midg; midg,igrid,midg 1.0948253E-09 -5.0281640E-10 1,midg,midg; igrid,midg,midg 9.4834518E-10 -7.1473694E-10 gauss-seidel spectral radius is 0.9852347 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 23:45:40 rms-change max change #iterations 0.1102555 17.57335 at 10iterations 9.1160238E-03 1.499901 at 20iterations 7.3660433E-04 0.1033287 at 30iterations 6.3268628E-05 9.6934438E-03 at 40iterations 6.4224264E-06 9.9396706E-04 at 50iterations finished qdiffx linear iterations at : 23:45:43 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 6.4224264E-06 9.9396706E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 23:45:43 3.475u 0.183s 0:03.96 92.1% 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 Sun Oct 9 2011 at 23:45:43 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 = 3141 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: 1.772908 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): -30.12600 30.11400 ymin,ymax (A): 7.942000 61.88600 zmin,zma (A): 25.04600 76.19600 x,y,z range (A): 60.24000 53.94400 51.15000 scale (grids/A): 1.772908 object centre (A): -5.9995651E-03 34.91400 50.62100 number of atom coordinates read : 3141 total number of charged atoms : 2996 net assigned charge : 0.5000069 assigned positive charge : 472.9330 centred at (gu) : 90.01488 87.05528 87.75935 assigned negative charge : -472.4342 centred at (gu) : 90.09026 87.12368 88.10856 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29023 grid for indexing accessible points = 1.400000 m= 25245 mr = 53871 m= 3019 mr = 17556 m= 103 mr = 1605 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1549 time to turn everything in is 0.4000000 number of dielectric boundary points 35071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 284 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23368 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) : 0.5909695 object centre at (A) : -5.9995651E-03 34.91400 50.62100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8812906E-03 -3.3246831E-03 midg,1,midg; midg,igrid,midg 8.9757638E-03 7.4118786E-03 1,midg,midg; igrid,midg,midg 1.3599880E-02 -7.3440541E-03 gauss-seidel spectral radius is 0.9984955 estimated iterations to convergence 204 setup time was (sec) 0.6200000 now iterating at: 23:45:44 rms-change max change #iterations 4.101001 188.8361 at 10iterations 1.838251 62.87206 at 20iterations 0.8252811 28.53635 at 30iterations 0.3730310 13.58619 at 40iterations 0.1676091 5.282852 at 50iterations 7.5608023E-02 2.820435 at 60iterations 3.4074176E-02 1.143240 at 70iterations 1.5314779E-02 0.5184898 at 80iterations 6.8780123E-03 0.2134466 at 90iterations 3.1135217E-03 0.1069527 at 100iterations 1.4069447E-03 4.6535492E-02 at 110iterations 6.3436059E-04 1.9845963E-02 at 120iterations finished qdiffx linear iterations at : 23:45:51 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 6.3436059E-04 1.9845963E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 23:45:52 7.967u 0.198s 0:08.42 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 Sun Oct 9 2011 at 23:45:52 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 = 3141 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: 2.659363 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): -30.12600 30.11400 ymin,ymax (A): 7.942000 61.88600 zmin,zma (A): 25.04600 76.19600 x,y,z range (A): 60.24000 53.94400 51.15000 scale (grids/A): 2.659363 object centre (A): -5.9995651E-03 34.91400 50.62100 number of atom coordinates read : 3141 total number of charged atoms : 2996 net assigned charge : 0.5000069 assigned positive charge : 472.9330 centred at (gu) : 90.02222 85.58274 86.63882 assigned negative charge : -472.4342 centred at (gu) : 90.13532 85.68541 87.16280 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29023 grid for indexing accessible points = 1.400000 m= 85828 mr = 131896 m= 26119 mr = 68063 m= 4810 mr = 19813 m= 436 mr = 3340 m= 8 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 5480 time to turn everything in is 0.9700000 number of dielectric boundary points 79002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 23960 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) : 1.772908 object centre at (A) : -5.9995651E-03 34.91400 50.62100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1374331 9.7263996E-03 midg,1,midg; midg,igrid,midg 9.0704367E-02 0.1090504 1,midg,midg; igrid,midg,midg 0.1329229 -8.0367438E-02 gauss-seidel spectral radius is 0.9992437 estimated iterations to convergence 287 setup time was (sec) 1.210000 now iterating at: 23:45:53 rms-change max change #iterations 10.17861 346.0807 at 10iterations 5.989326 153.0770 at 20iterations 3.496137 77.58034 at 30iterations 2.030591 43.36510 at 40iterations 1.174765 22.64272 at 50iterations 0.6787612 14.91317 at 60iterations 0.3919391 7.128693 at 70iterations 0.2249492 4.520882 at 80iterations 0.1292416 2.587948 at 90iterations 7.4228637E-02 1.371140 at 100iterations 4.2515013E-02 0.9256310 at 110iterations 2.4290448E-02 0.5090523 at 120iterations 1.3916989E-02 0.2999554 at 130iterations 7.9578338E-03 0.1616969 at 140iterations 4.5585376E-03 8.7736130E-02 at 150iterations 2.6019642E-03 4.5684814E-02 at 160iterations 1.4887787E-03 2.7359009E-02 at 170iterations 8.5037528E-04 1.5301704E-02 at 180iterations finished qdiffx linear iterations at : 23:46:05 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 8.5037528E-04 1.5301704E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 23:46:05 12.778u 0.201s 0:13.23 98.0% 0+0k 0+0io 0pf+0w