Wed Dec 21 14:21:22 PST 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 Wed Dec 21 2011 at 14:21:22 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 = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6023790 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): -24.13800 34.96100 ymin,ymax (A): -18.87800 20.70500 zmin,zma (A): -2.896000 38.70800 x,y,z range (A): 59.09900 39.58300 41.60400 scale (grids/A): 0.6023790 object centre (A): 5.411501 0.9134998 17.90600 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 2.000005 assigned positive charge : 287.8241 centred at (gu) : 89.71725 90.18311 90.38654 assigned negative charge : -285.8243 centred at (gu) : 89.72449 90.29896 90.54411 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4852 nv = 96 ne = 84 npr = 39847 no. pairs analyzed = 39847 no. exposed pairs = 2439 no. arc points = 16874 no. surface atoms = 837 nbur = 1125 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 183 mr = 2640 m= 0 mr = 11 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2500000 number of dielectric boundary points 2384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1747 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 5882 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9768909E-09 -4.0337786E-09 midg,1,midg; midg,igrid,midg 4.0910830E-09 -2.5461515E-09 1,midg,midg; igrid,midg,midg 1.2427288E-09 7.0412787E-10 gauss-seidel spectral radius is 0.9856814 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 14:21:23 rms-change max change #iterations 9.2608757E-02 15.04263 at 10iterations 7.9826163E-03 1.362766 at 20iterations 6.7376782E-04 0.1149082 at 30iterations 5.8167167E-05 9.2773438E-03 at 40iterations 4.8505954E-06 7.7819824E-04 at 50iterations finished qdiffx linear iterations at : 14:21:27 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 4.8505954E-06 7.7819824E-04 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 14:21:32 4.657u 0.369s 0:10.16 49.3% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:32 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 = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.807137 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): -24.13800 34.96100 ymin,ymax (A): -18.87800 20.70500 zmin,zma (A): -2.896000 38.70800 x,y,z range (A): 59.09900 39.58300 41.60400 scale (grids/A): 1.807137 object centre (A): 5.411501 0.9134998 17.90600 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 2.000005 assigned positive charge : 287.8241 centred at (gu) : 89.15192 90.54926 91.16015 assigned negative charge : -285.8243 centred at (gu) : 89.17353 90.89703 91.63251 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52537 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16874 grid for indexing accessible points = 1.400000 m= 18617 mr = 36173 m= 2239 mr = 14017 m= 61 mr = 1287 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.4200000 number of dielectric boundary points 21977 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14321 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) : 0.6023790 object centre at (A) : 5.411501 0.9134998 17.90600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3129585E-03 -8.1110941E-03 midg,1,midg; midg,igrid,midg 2.4451516E-03 -6.1620641E-03 1,midg,midg; igrid,midg,midg 3.8811296E-02 3.1891249E-02 gauss-seidel spectral radius is 0.9984075 estimated iterations to convergence 199 setup time was (sec) 0.7200000 now iterating at: 14:21:34 rms-change max change #iterations 3.197118 157.1293 at 10iterations 1.402232 57.24219 at 20iterations 0.6195219 23.11013 at 30iterations 0.2727444 10.19812 at 40iterations 0.1203167 4.400571 at 50iterations 5.2924592E-02 2.237669 at 60iterations 2.3261502E-02 0.9304702 at 70iterations 1.0249428E-02 0.4132156 at 80iterations 4.5249830E-03 0.1610098 at 90iterations 1.9902054E-03 7.3347092E-02 at 100iterations 8.7968924E-04 3.1461716E-02 at 110iterations 3.8768831E-04 1.5713692E-02 at 120iterations finished qdiffx linear iterations at : 14:21:44 total time elapsed so far: 10.67000 # loops : 120 mean,max change (kT/e) : 3.8768831E-04 1.5713692E-02 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 14:21:46 10.853u 0.457s 0:14.57 77.5% 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 Wed Dec 21 2011 at 14:21:49 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 = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.710706 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): -24.13800 34.96100 ymin,ymax (A): -18.87800 20.70500 zmin,zma (A): -2.896000 38.70800 x,y,z range (A): 59.09900 39.58300 41.60400 scale (grids/A): 2.710706 object centre (A): 5.411501 0.9134998 17.90600 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 2.000005 assigned positive charge : 287.8241 centred at (gu) : 88.72792 90.82400 91.74008 assigned negative charge : -285.8243 centred at (gu) : 88.76030 91.34563 92.44889 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 121349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16874 grid for indexing accessible points = 1.400000 m= 61911 mr = 87556 m= 20456 mr = 51239 m= 3644 mr = 16493 m= 254 mr = 2566 m= 4 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 807 time to turn everything in is 1.080000 number of dielectric boundary points 49656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 14639 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) : 1.807137 object centre at (A) : 5.411501 0.9134998 17.90600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9663105E-02 -7.0631765E-02 midg,1,midg; midg,igrid,midg 1.1904059E-02 -5.5081837E-02 1,midg,midg; igrid,midg,midg 0.4392700 0.3196103 gauss-seidel spectral radius is 0.9991763 estimated iterations to convergence 275 setup time was (sec) 1.390000 now iterating at: 14:21:52 rms-change max change #iterations 7.844004 372.4407 at 10iterations 4.455305 168.0730 at 20iterations 2.516963 65.26306 at 30iterations 1.408462 35.70047 at 40iterations 0.7877291 17.34534 at 50iterations 0.4393458 9.596667 at 60iterations 0.2446444 5.480509 at 70iterations 0.1368108 2.958947 at 80iterations 7.6050669E-02 1.646274 at 90iterations 4.2319082E-02 0.9387741 at 100iterations 2.3556866E-02 0.5290613 at 110iterations 1.3109376E-02 0.2693987 at 120iterations 7.2814985E-03 0.1558895 at 130iterations 4.0598921E-03 0.1084213 at 140iterations 2.2581420E-03 5.1164627E-02 at 150iterations 1.2554359E-03 2.7626038E-02 at 160iterations 6.9783995E-04 1.5399933E-02 at 170iterations 3.8852872E-04 8.2111359E-03 at 180iterations finished qdiffx linear iterations at : 14:22:06 total time elapsed so far: 16.25000 # loops : 180 mean,max change (kT/e) : 3.8852872E-04 8.2111359E-03 energy calculations done at 16.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.42000 DelPhi exited at 14:22:12 16.422u 0.466s 0:23.29 72.4% 0+0k 0+0io 0pf+0w