Sat Oct 8 17:02:55 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 Sat Oct 8 2011 at 17:02:55 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4906 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4870841 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): -3.937000 62.74400 ymin,ymax (A): -30.27000 30.87400 zmin,zma (A): -23.79400 49.29400 x,y,z range (A): 66.68100 61.14400 73.08800 scale (grids/A): 0.4870841 object centre (A): 29.40350 0.3020000 12.75000 number of atom coordinates read : 4906 total number of charged atoms : 4750 net assigned charge : -12.99997 assigned positive charge : 749.2564 centred at (gu) : 90.94528 91.24338 90.05596 assigned negative charge : -762.2620 centred at (gu) : 90.95535 91.19590 90.07239 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7539 nv = 96 ne = 84 npr = 94782 no. pairs analyzed = 94782 no. exposed pairs = 6668 no. arc points = 47394 no. surface atoms = 2198 nbur = 2708 mkacc time = 0.2000000 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= 259 mr = 3640 m= 0 mr = 6 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4474 ## 812 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 10182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5404871E-11 -7.8899096E-11 midg,1,midg; midg,igrid,midg -7.7037855E-11 -2.2067917E-11 1,midg,midg; igrid,midg,midg -4.0643277E-11 -9.2465036E-11 gauss-seidel spectral radius is 0.9784808 estimated iterations to convergence 56 setup time was (sec) 0.6700000 now iterating at: 17:02:56 rms-change max change #iterations 5.3465065E-02 9.724442 at 10iterations 2.7565781E-03 0.4299316 at 20iterations 3.1144181E-04 6.5864563E-02 at 30iterations 8.1762621E-05 1.8746376E-02 at 40iterations 2.3436352E-05 5.3977966E-03 at 50iterations finished qdiffx linear iterations at : 17:02:58 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.3436352E-05 5.3977966E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 17:02:59 3.438u 0.223s 0:03.94 92.6% 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 Sat Oct 8 2011 at 17:02:59 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4906 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.461252 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): -3.937000 62.74400 ymin,ymax (A): -30.27000 30.87400 zmin,zma (A): -23.79400 49.29400 x,y,z range (A): 66.68100 61.14400 73.08800 scale (grids/A): 1.461252 object centre (A): 29.40350 0.3020000 12.75000 number of atom coordinates read : 4906 total number of charged atoms : 4750 net assigned charge : -12.99997 assigned positive charge : 749.2564 centred at (gu) : 92.83453 93.72839 90.16657 assigned negative charge : -762.2620 centred at (gu) : 92.86592 93.58768 90.21714 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85080 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47394 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 23281 mr = 55755 m= 1714 mr = 14760 m= 30 mr = 659 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 583 time to turn everything in is 0.6000000 number of dielectric boundary points 38931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 731 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 35034 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) : 0.4870841 object centre at (A) : 29.40350 0.3020000 12.75000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5841494E-03 -2.7222829E-02 midg,1,midg; midg,igrid,midg -9.3008652E-03 -5.9787370E-03 1,midg,midg; igrid,midg,midg 2.0160209E-03 -3.3678303E-03 gauss-seidel spectral radius is 0.9979176 estimated iterations to convergence 174 setup time was (sec) 0.9000000 now iterating at: 17:03:00 rms-change max change #iterations 3.498044 136.2219 at 10iterations 1.365293 46.98709 at 20iterations 0.5349655 20.66820 at 30iterations 0.2095765 7.519228 at 40iterations 8.2075119E-02 2.910975 at 50iterations 3.2255311E-02 1.253704 at 60iterations 1.2669844E-02 0.4396915 at 70iterations 5.0027422E-03 0.1856804 at 80iterations 1.9826472E-03 6.7152023E-02 at 90iterations 7.9915329E-04 2.7014256E-02 at 100iterations 3.3355522E-04 1.3336182E-02 at 110iterations 1.4810513E-04 5.9509277E-03 at 120iterations finished qdiffx linear iterations at : 17:03:06 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.4810513E-04 5.9509277E-03 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 17:03:07 7.657u 0.224s 0:08.18 96.2% 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 Sat Oct 8 2011 at 17:03:07 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4906 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.191878 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): -3.937000 62.74400 ymin,ymax (A): -30.27000 30.87400 zmin,zma (A): -23.79400 49.29400 x,y,z range (A): 66.68100 61.14400 73.08800 scale (grids/A): 2.191878 object centre (A): 29.40350 0.3020000 12.75000 number of atom coordinates read : 4906 total number of charged atoms : 4750 net assigned charge : -12.99997 assigned positive charge : 749.2564 centred at (gu) : 94.25117 95.59236 90.24941 assigned negative charge : -762.2620 centred at (gu) : 94.29897 95.38143 90.32575 start vw surface at 0.2000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 198212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47394 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 85094 mr = 137924 m= 19491 mr = 64417 m= 2338 mr = 13613 m= 84 mr = 1358 m= 0 mr = 16 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 2001 time to turn everything in is 1.430000 number of dielectric boundary points 87891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 37847 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) : 1.461252 object centre at (A) : 29.40350 0.3020000 12.75000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2376117 -0.4595927 midg,1,midg; midg,igrid,midg -0.2740504 -0.1014842 1,midg,midg; igrid,midg,midg 2.7144721E-02 -0.1004516 gauss-seidel spectral radius is 0.9990969 estimated iterations to convergence 263 setup time was (sec) 1.750000 now iterating at: 17:03:09 rms-change max change #iterations 9.839209 267.6272 at 10iterations 5.540808 150.9105 at 20iterations 3.093197 81.46961 at 30iterations 1.717047 39.20364 at 40iterations 0.9469112 20.16194 at 50iterations 0.5210189 10.66779 at 60iterations 0.2857575 5.868438 at 70iterations 0.1561793 3.299764 at 80iterations 8.5451655E-02 1.615875 at 90iterations 4.6605933E-02 1.057815 at 100iterations 2.5400592E-02 0.4851685 at 110iterations 1.3847231E-02 0.2776001 at 120iterations 7.5374013E-03 0.1604996 at 130iterations 4.0997039E-03 7.7020168E-02 at 140iterations 2.2350168E-03 4.9350739E-02 at 150iterations 1.2203400E-03 2.3906112E-02 at 160iterations 6.6945259E-04 1.2240566E-02 at 170iterations 3.6889329E-04 7.5640678E-03 at 180iterations finished qdiffx linear iterations at : 17:03:19 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 3.6889329E-04 7.5640678E-03 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 17:03:20 12.471u 0.242s 0:12.98 97.9% 0+0k 0+0io 0pf+0w