Wed Dec 21 14:21:44 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+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 Wed Dec 21 2011 at 14:21:45 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: 272 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6393334 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): -4.070000 34.99300 ymin,ymax (A): -3.964000 49.46700 zmin,zma (A): -24.03900 31.64400 x,y,z range (A): 39.06300 53.43100 55.68300 scale (grids/A): 0.6393334 object centre (A): 15.46150 22.75150 3.802500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.0260 centred at (gu) : 90.36012 92.35625 89.99352 assigned negative charge : -287.0263 centred at (gu) : 90.42539 92.42711 89.93214 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5559 nv = 96 ne = 84 npr = 39995 no. pairs analyzed = 39995 no. exposed pairs = 2477 no. arc points = 17373 no. surface atoms = 841 nbur = 1121 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 267 mr = 3094 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.1700000 number of dielectric boundary points 2694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1766 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6583639E-10 1.0979242E-08 midg,1,midg; midg,igrid,midg 7.1876154E-09 -5.1613469E-10 1,midg,midg; igrid,midg,midg 1.0485983E-08 3.3355754E-10 gauss-seidel spectral radius is 0.9872697 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 14:21:46 rms-change max change #iterations 0.1261500 25.37318 at 10iterations 1.2398375E-02 2.081848 at 20iterations 1.2028385E-03 0.1747949 at 30iterations 1.1625153E-04 1.8647194E-02 at 40iterations 1.1935877E-05 2.0847321E-03 at 50iterations finished qdiffx linear iterations at : 14:21:50 total time elapsed so far: 4.440000 # loops : 50 mean,max change (kT/e) : 1.1935877E-05 2.0847321E-03 energy calculations done at 4.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 14:22:20 4.579u 0.262s 0:35.81 13.4% 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 14:22:22 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: 272 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918000 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): -4.070000 34.99300 ymin,ymax (A): -3.964000 49.46700 zmin,zma (A): -24.03900 31.64400 x,y,z range (A): 39.06300 53.43100 55.68300 scale (grids/A): 1.918000 object centre (A): 15.46150 22.75150 3.802500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.0260 centred at (gu) : 91.08049 97.06884 89.98048 assigned negative charge : -287.0263 centred at (gu) : 91.27634 97.28134 89.79661 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 59803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17373 grid for indexing accessible points = 1.400000 m= 22262 mr = 41382 m= 3146 mr = 17085 m= 140 mr = 1965 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1229 time to turn everything in is 0.3000000 number of dielectric boundary points 24867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14420 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) : 0.6393334 object centre at (A) : 15.46150 22.75150 3.802500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3901294E-02 1.9052841E-02 midg,1,midg; midg,igrid,midg 2.9947238E-02 4.2130388E-03 1,midg,midg; igrid,midg,midg 4.0437635E-03 -1.9659975E-03 gauss-seidel spectral radius is 0.9985757 estimated iterations to convergence 210 setup time was (sec) 0.5500000 now iterating at: 14:22:24 rms-change max change #iterations 3.677860 176.2348 at 10iterations 1.692631 62.86018 at 20iterations 0.7810926 32.59718 at 30iterations 0.3597315 13.28476 at 40iterations 0.1658800 5.922475 at 50iterations 7.6077051E-02 2.505203 at 60iterations 3.4978203E-02 1.304094 at 70iterations 1.6146941E-02 0.5391493 at 80iterations 7.4507659E-03 0.2584274 at 90iterations 3.4246591E-03 0.1079812 at 100iterations 1.5875751E-03 6.4667940E-02 at 110iterations 7.2760956E-04 2.5899887E-02 at 120iterations finished qdiffx linear iterations at : 14:22:33 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 7.2760956E-04 2.5899887E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 14:22:43 9.781u 0.287s 0:21.55 46.6% 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 Wed Dec 21 2011 at 14:22:46 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: 272 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.877000 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): -4.070000 34.99300 ymin,ymax (A): -3.964000 49.46700 zmin,zma (A): -24.03900 31.64400 x,y,z range (A): 39.06300 53.43100 55.68300 scale (grids/A): 2.877000 object centre (A): 15.46150 22.75150 3.802500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.0260 centred at (gu) : 91.62065 100.6033 89.97091 assigned negative charge : -287.0263 centred at (gu) : 91.91463 100.9221 89.69498 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 137877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17373 grid for indexing accessible points = 1.400000 m= 72077 mr = 99834 m= 26133 mr = 60169 m= 5469 mr = 21614 m= 655 mr = 4165 m= 35 mr = 415 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 4036 time to turn everything in is 0.8100000 number of dielectric boundary points 56036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 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) : 1.918000 object centre at (A) : 15.46150 22.75150 3.802500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.068709 9.7438999E-02 midg,1,midg; midg,igrid,midg 0.2942339 -1.7867953E-02 1,midg,midg; igrid,midg,midg 1.4678505E-02 -9.5487079E-03 gauss-seidel spectral radius is 0.9992285 estimated iterations to convergence 284 setup time was (sec) 1.100000 now iterating at: 14:22:49 rms-change max change #iterations 8.657054 346.1873 at 10iterations 4.997567 129.7749 at 20iterations 2.849435 65.84254 at 30iterations 1.629540 41.79366 at 40iterations 0.9294913 19.49766 at 50iterations 0.5280336 11.62058 at 60iterations 0.3000899 7.036270 at 70iterations 0.1701755 3.509766 at 80iterations 9.6740313E-02 2.063335 at 90iterations 5.4971743E-02 1.177906 at 100iterations 3.1150075E-02 0.6433945 at 110iterations 1.7679436E-02 0.3478413 at 120iterations 1.0027229E-02 0.2019205 at 130iterations 5.6899483E-03 0.1261330 at 140iterations 3.2238793E-03 6.6135883E-02 at 150iterations 1.8250496E-03 3.6983490E-02 at 160iterations 1.0368904E-03 2.6081085E-02 at 170iterations 5.8797462E-04 1.2168884E-02 at 180iterations finished qdiffx linear iterations at : 14:23:05 total time elapsed so far: 17.52000 # loops : 180 mean,max change (kT/e) : 5.8797462E-04 1.2168884E-02 energy calculations done at 17.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.65000 DelPhi exited at 14:23:08 17.650u 0.289s 0:22.53 79.5% 0+0k 0+0io 0pf+0w