Mon Oct 10 14:07:25 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 Mon Oct 10 2011 at 14:07:25 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 = 5882 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4856687 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): 14.81000 80.48500 ymin,ymax (A): 18.45400 85.09000 zmin,zma (A): -5.157000 68.14400 x,y,z range (A): 65.67500 66.63600 73.30099 scale (grids/A): 0.4856687 object centre (A): 47.64750 51.77200 31.49350 number of atom coordinates read : 5882 total number of charged atoms : 5714 net assigned charge : 0.5000445 assigned positive charge : 882.6202 centred at (gu) : 90.07887 89.41766 90.68286 assigned negative charge : -882.1279 centred at (gu) : 90.02474 89.43694 90.82542 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8733 nv = 96 ne = 84 npr = 117079 no. pairs analyzed = 117079 no. exposed pairs = 7600 no. arc points = 52582 no. surface atoms = 2554 nbur = 3328 mkacc time = 0.2700000 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 = 1.764000 m= 284 mr = 4376 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4975 ## 841 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11786 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2340409E-10 -1.8023262E-10 midg,1,midg; midg,igrid,midg 2.7496842E-11 -1.4372579E-11 1,midg,midg; igrid,midg,midg -5.2532124E-11 6.0719894E-11 gauss-seidel spectral radius is 0.9784112 estimated iterations to convergence 56 setup time was (sec) 0.7800000 now iterating at: 14:07:26 rms-change max change #iterations 5.5634186E-02 9.506691 at 10iterations 3.0864715E-03 0.4637756 at 20iterations 3.9129675E-04 9.8121643E-02 at 30iterations 1.0275640E-04 2.5588989E-02 at 40iterations 3.1379383E-05 7.2574615E-03 at 50iterations finished qdiffx linear iterations at : 14:07:28 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.1379383E-05 7.2574615E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 14:07:29 3.534u 0.184s 0:04.21 88.1% 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 Mon Oct 10 2011 at 14:07:29 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 = 5882 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.457006 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): 14.81000 80.48500 ymin,ymax (A): 18.45400 85.09000 zmin,zma (A): -5.157000 68.14400 x,y,z range (A): 65.67500 66.63600 73.30099 scale (grids/A): 1.457006 object centre (A): 47.64750 51.77200 31.49350 number of atom coordinates read : 5882 total number of charged atoms : 5714 net assigned charge : 0.5000445 assigned positive charge : 882.6202 centred at (gu) : 90.23523 88.25119 92.04742 assigned negative charge : -882.1279 centred at (gu) : 90.07390 88.31113 92.47578 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 99179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 27927 mr = 66988 m= 1999 mr = 17760 m= 32 mr = 594 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 277 time to turn everything in is 0.7000000 number of dielectric boundary points 43795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 830 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 42011 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) : 0.4856687 object centre at (A) : 47.64750 51.77200 31.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9096928E-02 -3.5290938E-02 midg,1,midg; midg,igrid,midg 4.3384411E-04 -8.0804648E-03 1,midg,midg; igrid,midg,midg 1.3542067E-03 7.5108944E-03 gauss-seidel spectral radius is 0.9979994 estimated iterations to convergence 178 setup time was (sec) 0.9900000 now iterating at: 14:07:30 rms-change max change #iterations 3.796492 188.4999 at 10iterations 1.514399 47.72423 at 20iterations 0.6046087 18.86185 at 30iterations 0.2428302 7.739308 at 40iterations 9.6946739E-02 2.891556 at 50iterations 3.8879585E-02 1.313410 at 60iterations 1.5603000E-02 0.4944615 at 70iterations 6.2727914E-03 0.1997833 at 80iterations 2.5605061E-03 8.4585190E-02 at 90iterations 1.0657846E-03 3.4883499E-02 at 100iterations 4.7022151E-04 2.0080566E-02 at 110iterations 2.2587753E-04 1.0040283E-02 at 120iterations finished qdiffx linear iterations at : 14:07:37 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.2587753E-04 1.0040283E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 14:07:38 7.684u 0.213s 0:08.68 90.8% 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 Mon Oct 10 2011 at 14:07:38 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 = 5882 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.185509 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): 14.81000 80.48500 ymin,ymax (A): 18.45400 85.09000 zmin,zma (A): -5.157000 68.14400 x,y,z range (A): 65.67500 66.63600 73.30099 scale (grids/A): 2.185509 object centre (A): 47.64750 51.77200 31.49350 number of atom coordinates read : 5882 total number of charged atoms : 5714 net assigned charge : 0.5000445 assigned positive charge : 882.6202 centred at (gu) : 90.35220 87.37668 93.07053 assigned negative charge : -882.1279 centred at (gu) : 90.11081 87.46652 93.71369 start vw surface at 0.2700000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 231217 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 101595 mr = 165367 m= 23444 mr = 77540 m= 2571 mr = 15938 m= 75 mr = 1229 m= 0 mr = 3 time to grow re-entrant surface = 0.9900001 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 1.720000 number of dielectric boundary points 98825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 45479 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) : 1.457006 object centre at (A) : 47.64750 51.77200 31.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4954430 -0.9429461 midg,1,midg; midg,igrid,midg 1.3317799E-02 -0.1725079 1,midg,midg; igrid,midg,midg 5.8676846E-02 9.0110749E-02 gauss-seidel spectral radius is 0.9991651 estimated iterations to convergence 273 setup time was (sec) 2.050000 now iterating at: 14:07:40 rms-change max change #iterations 10.83910 352.8585 at 10iterations 6.265084 151.1035 at 20iterations 3.600184 81.80989 at 30iterations 2.058142 44.89983 at 40iterations 1.171523 24.97087 at 50iterations 0.6649827 17.30415 at 60iterations 0.3745267 9.738531 at 70iterations 0.2113680 4.096359 at 80iterations 0.1187685 2.441162 at 90iterations 6.6822007E-02 1.364574 at 100iterations 3.7429228E-02 0.7100048 at 110iterations 2.0972118E-02 0.3832712 at 120iterations 1.1734405E-02 0.2087545 at 130iterations 6.5761828E-03 0.1349640 at 140iterations 3.6815421E-03 6.8413258E-02 at 150iterations 2.0588667E-03 3.7776947E-02 at 160iterations 1.1548928E-03 2.0191193E-02 at 170iterations 6.4853433E-04 1.1703968E-02 at 180iterations finished qdiffx linear iterations at : 14:07:51 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 6.4853433E-04 1.1703968E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 14:07:52 13.009u 0.243s 0:14.14 93.6% 0+0k 0+0io 0pf+0w