Mon Oct 10 14:14:10 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 Mon Oct 10 2011 at 14:14:10 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6189259 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): -12.01200 44.75200 ymin,ymax (A): -10.47400 47.04500 zmin,zma (A): -27.79300 19.44700 x,y,z range (A): 56.76400 57.51900 47.24000 scale (grids/A): 0.6189259 object centre (A): 16.37000 18.28550 -4.172999 number of atom coordinates read : 2778 total number of charged atoms : 2603 net assigned charge : 6.500030 assigned positive charge : 418.0525 centred at (gu) : 90.18440 90.44704 91.28585 assigned negative charge : -411.5533 centred at (gu) : 90.18849 90.40775 91.24001 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7295 nv = 96 ne = 84 npr = 54665 no. pairs analyzed = 54665 no. exposed pairs = 3620 no. arc points = 25630 no. surface atoms = 1202 nbur = 1576 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 3898 m= 0 mr = 34 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2575 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8734 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4491622E-09 1.0750918E-08 midg,1,midg; midg,igrid,midg 2.1094797E-09 8.4505398E-09 1,midg,midg; igrid,midg,midg 5.0732138E-09 4.9073674E-09 gauss-seidel spectral radius is 0.9865040 estimated iterations to convergence 70 setup time was (sec) 0.6800000 now iterating at: 14:14:11 rms-change max change #iterations 0.1328430 19.96307 at 10iterations 1.1955101E-02 1.837593 at 20iterations 1.1149348E-03 0.1901131 at 30iterations 1.1611725E-04 1.7349243E-02 at 40iterations 2.0840640E-05 3.5085678E-03 at 50iterations finished qdiffx linear iterations at : 14:14:14 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 2.0840640E-05 3.5085678E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 14:14:15 4.260u 0.205s 0:05.24 85.1% 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 14:14:15 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.856778 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): -12.01200 44.75200 ymin,ymax (A): -10.47400 47.04500 zmin,zma (A): -27.79300 19.44700 x,y,z range (A): 56.76400 57.51900 47.24000 scale (grids/A): 1.856778 object centre (A): 16.37000 18.28550 -4.172999 number of atom coordinates read : 2778 total number of charged atoms : 2603 net assigned charge : 6.500030 assigned positive charge : 418.0525 centred at (gu) : 90.55259 91.34068 93.85655 assigned negative charge : -411.5533 centred at (gu) : 90.56520 91.22274 93.71962 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 78570 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25630 grid for indexing accessible points = 1.400000 m= 28962 mr = 53875 m= 4703 mr = 21126 m= 310 mr = 2762 m= 8 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 34674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20427 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) : 0.6189259 object centre at (A) : 16.37000 18.28550 -4.172999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3174086E-03 2.6301311E-02 midg,1,midg; midg,igrid,midg 3.9505986E-03 2.7022125E-02 1,midg,midg; igrid,midg,midg 1.6656898E-02 -9.5647998E-04 gauss-seidel spectral radius is 0.9985874 estimated iterations to convergence 211 setup time was (sec) 1.120000 now iterating at: 14:14:16 rms-change max change #iterations 4.201515 199.0236 at 10iterations 1.938181 70.73215 at 20iterations 0.8940891 30.94287 at 30iterations 0.4123864 14.46271 at 40iterations 0.1910182 6.935067 at 50iterations 8.7990575E-02 2.830873 at 60iterations 4.0814158E-02 1.416639 at 70iterations 1.8810831E-02 0.5723982 at 80iterations 8.7395739E-03 0.2845018 at 90iterations 4.0406669E-03 0.1294351 at 100iterations 1.8652426E-03 6.7798615E-02 at 110iterations 8.5980166E-04 2.7478218E-02 at 120iterations finished qdiffx linear iterations at : 14:14:25 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 8.5980166E-04 2.7478218E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.750000 DelPhi exited at 14:14:25 9.750u 0.265s 0:10.47 95.6% 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 Mon Oct 10 2011 at 14:14:26 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2778 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.785167 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): -12.01200 44.75200 ymin,ymax (A): -10.47400 47.04500 zmin,zma (A): -27.79300 19.44700 x,y,z range (A): 56.76400 57.51900 47.24000 scale (grids/A): 2.785167 object centre (A): 16.37000 18.28550 -4.172999 number of atom coordinates read : 2778 total number of charged atoms : 2603 net assigned charge : 6.500030 assigned positive charge : 418.0525 centred at (gu) : 90.82857 92.01077 95.78483 assigned negative charge : -411.5533 centred at (gu) : 90.84767 91.83411 95.57929 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 181529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25630 grid for indexing accessible points = 1.400000 m= 92580 mr = 130452 m= 34133 mr = 75307 m= 8221 mr = 27112 m= 1270 mr = 5932 m= 71 mr = 833 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 78152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 20824 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) : 1.856778 object centre at (A) : 16.37000 18.28550 -4.172999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6835360E-02 0.3106619 midg,1,midg; midg,igrid,midg 4.8254900E-02 0.2954598 1,midg,midg; igrid,midg,midg 0.1556480 -0.1158094 gauss-seidel spectral radius is 0.9992529 estimated iterations to convergence 289 setup time was (sec) 2.260000 now iterating at: 14:14:28 rms-change max change #iterations 10.08692 422.9067 at 10iterations 5.943661 138.4993 at 20iterations 3.471913 76.22235 at 30iterations 2.019624 45.46007 at 40iterations 1.171149 23.30089 at 50iterations 0.6760780 13.44161 at 60iterations 0.3907775 7.259846 at 70iterations 0.2248974 4.612413 at 80iterations 0.1293870 2.478912 at 90iterations 7.4375749E-02 1.322414 at 100iterations 4.2739715E-02 0.8982468 at 110iterations 2.4568971E-02 0.4440994 at 120iterations 1.4123895E-02 0.2631187 at 130iterations 8.1149843E-03 0.1577148 at 140iterations 4.6663051E-03 9.1832399E-02 at 150iterations 2.6863546E-03 4.5169830E-02 at 160iterations 1.5586007E-03 2.7102470E-02 at 170iterations 9.0964040E-04 1.6628027E-02 at 180iterations finished qdiffx linear iterations at : 14:14:41 total time elapsed so far: 15.65000 # loops : 180 mean,max change (kT/e) : 9.0964040E-04 1.6628027E-02 energy calculations done at 15.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.93000 DelPhi exited at 14:14:42 15.927u 0.288s 0:16.53 98.0% 0+0k 0+0io 0pf+0w