Sat Oct 15 12:13:29 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 15 2011 at 12:13:29 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3507 !!! WARNING: GLM 89 has a net charge of -0.0940 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: 0.5391163 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): -46.60700 7.404000 ymin,ymax (A): 172.6540 236.4780 zmin,zma (A): 78.27400 144.3080 x,y,z range (A): 54.01100 63.82402 66.03400 scale (grids/A): 0.5391163 object centre (A): -19.60150 204.5660 111.2910 number of atom coordinates read : 3507 total number of charged atoms : 3358 net assigned charge : 11.40604 assigned positive charge : 519.1970 centred at (gu) : 89.54388 90.05815 90.18787 assigned negative charge : -507.7931 centred at (gu) : 89.44606 89.99460 90.30986 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6727 nv = 96 ne = 84 npr = 68120 no. pairs analyzed = 68120 no. exposed pairs = 4768 no. arc points = 33662 no. surface atoms = 1581 nbur = 1926 mkacc time = 0.1200000 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 = 1.568000 m= 280 mr = 3309 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2400000 number of dielectric boundary points 3687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3294 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1925474E-09 -1.8928061E-10 midg,1,midg; midg,igrid,midg 1.6902281E-10 9.2883901E-10 1,midg,midg; igrid,midg,midg -4.1111510E-11 9.9302611E-10 gauss-seidel spectral radius is 0.9823182 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 12:13:30 rms-change max change #iterations 7.4795097E-02 13.41439 at 10iterations 4.7442052E-03 0.8174680 at 20iterations 3.1607295E-04 4.5125961E-02 at 30iterations 2.3112818E-05 3.6144257E-03 at 40iterations 2.4069718E-06 2.9659271E-04 at 50iterations finished qdiffx linear iterations at : 12:13:33 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 2.4069718E-06 2.9659271E-04 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 12:13:34 3.502u 0.208s 0:04.18 88.5% 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 15 2011 at 12:13:34 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3507 !!! WARNING: GLM 89 has a net charge of -0.0940 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: 1.617349 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): -46.60700 7.404000 ymin,ymax (A): 172.6540 236.4780 zmin,zma (A): 78.27400 144.3080 x,y,z range (A): 54.01100 63.82402 66.03400 scale (grids/A): 1.617349 object centre (A): -19.60150 204.5660 111.2910 number of atom coordinates read : 3507 total number of charged atoms : 3358 net assigned charge : 11.40604 assigned positive charge : 519.1970 centred at (gu) : 88.63063 90.17296 90.56261 assigned negative charge : -507.7931 centred at (gu) : 88.33791 89.98354 90.92912 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33662 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22795 mr = 49663 m= 2311 mr = 15133 m= 74 mr = 1107 m= 0 mr = 1 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1096 time to turn everything in is 0.3700000 number of dielectric boundary points 34423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 25733 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) : 0.5391163 object centre at (A) : -19.60150 204.5660 111.2910 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7693984E-03 -1.0527360E-02 midg,1,midg; midg,igrid,midg 6.6539445E-03 2.2145914E-02 1,midg,midg; igrid,midg,midg -7.7048846E-04 1.1476531E-02 gauss-seidel spectral radius is 0.9982206 estimated iterations to convergence 188 setup time was (sec) 0.6100000 now iterating at: 12:13:35 rms-change max change #iterations 3.537659 181.1933 at 10iterations 1.479680 58.29844 at 20iterations 0.6218613 22.27417 at 30iterations 0.2605809 9.512616 at 40iterations 0.1088529 3.656101 at 50iterations 4.5801360E-02 1.668528 at 60iterations 1.9262616E-02 0.7016382 at 70iterations 8.1110289E-03 0.2824783 at 80iterations 3.3980825E-03 0.1200986 at 90iterations 1.4319893E-03 5.0989151E-02 at 100iterations 6.0447777E-04 2.0633698E-02 at 110iterations 2.5498209E-04 8.4037781E-03 at 120iterations finished qdiffx linear iterations at : 12:13:43 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 2.5498209E-04 8.4037781E-03 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 12:13:43 7.996u 0.303s 0:09.88 83.9% 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 15 2011 at 12:13:44 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3507 !!! WARNING: GLM 89 has a net charge of -0.0940 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: 2.426023 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): -46.60700 7.404000 ymin,ymax (A): 172.6540 236.4780 zmin,zma (A): 78.27400 144.3080 x,y,z range (A): 54.01100 63.82402 66.03400 scale (grids/A): 2.426023 object centre (A): -19.60150 204.5660 111.2910 number of atom coordinates read : 3507 total number of charged atoms : 3358 net assigned charge : 11.40604 assigned positive charge : 519.1970 centred at (gu) : 87.94562 90.25925 90.84368 assigned negative charge : -507.7931 centred at (gu) : 87.50685 89.97511 91.39384 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 174683 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33662 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 78760 mr = 122424 m= 22061 mr = 60760 m= 3571 mr = 16103 m= 247 mr = 2276 m= 2 mr = 85 m= 1 mr = 0 m= 1 mr = 0 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 3985 time to turn everything in is 0.9700000 number of dielectric boundary points 77679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 26830 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) : 1.617349 object centre at (A) : -19.60150 204.5660 111.2910 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2365590 -0.1234917 midg,1,midg; midg,igrid,midg 2.8053496E-02 0.4079510 1,midg,midg; igrid,midg,midg -7.6112129E-02 0.1311574 gauss-seidel spectral radius is 0.9991708 estimated iterations to convergence 274 setup time was (sec) 1.250000 now iterating at: 12:13:45 rms-change max change #iterations 9.219470 317.7217 at 10iterations 5.276093 113.8738 at 20iterations 3.002969 76.55980 at 30iterations 1.700678 42.93118 at 40iterations 0.9585328 19.01578 at 50iterations 0.5380116 11.15466 at 60iterations 0.3006188 6.552876 at 70iterations 0.1679391 3.418025 at 80iterations 9.4031155E-02 1.879644 at 90iterations 5.2518357E-02 0.9856033 at 100iterations 2.9154900E-02 0.6050224 at 110iterations 1.6291138E-02 0.3187790 at 120iterations 9.0847146E-03 0.1799736 at 130iterations 5.0476794E-03 9.5329285E-02 at 140iterations 2.8066156E-03 5.4689407E-02 at 150iterations 1.5595229E-03 2.9228210E-02 at 160iterations 8.6711237E-04 1.6416550E-02 at 170iterations 4.8255277E-04 9.4032288E-03 at 180iterations finished qdiffx linear iterations at : 12:13:58 total time elapsed so far: 14.44000 # loops : 180 mean,max change (kT/e) : 4.8255277E-04 9.4032288E-03 energy calculations done at 14.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.57000 DelPhi exited at 12:13:59 14.574u 0.273s 0:15.23 97.4% 0+0k 0+0io 0pf+0w