Mon Oct 10 13:55:58 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 13:55:58 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6991358 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): -0.3620000 45.67000 ymin,ymax (A): 35.28100 86.20100 zmin,zma (A): -23.63900 25.02500 x,y,z range (A): 46.03200 50.92001 48.66400 scale (grids/A): 0.6991358 object centre (A): 22.65400 60.74100 0.6929998 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 361.0473 centred at (gu) : 89.67296 90.03238 91.41135 assigned negative charge : -359.5475 centred at (gu) : 89.76376 90.22837 91.34971 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7845 nv = 96 ne = 84 npr = 47771 no. pairs analyzed = 47771 no. exposed pairs = 2965 no. arc points = 20575 no. surface atoms = 1000 nbur = 1359 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 493 mr = 4397 m= 6 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1999 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4457268E-08 5.1480530E-08 midg,1,midg; midg,igrid,midg 9.9896283E-08 -8.4954969E-08 1,midg,midg; igrid,midg,midg 5.5880882E-08 -3.1158471E-08 gauss-seidel spectral radius is 0.9893678 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 13:55:58 rms-change max change #iterations 0.2081182 29.16328 at 10iterations 2.5168033E-02 3.939255 at 20iterations 3.5761876E-03 0.4752808 at 30iterations 7.4314745E-04 0.1076622 at 40iterations 2.2365883E-04 3.3210754E-02 at 50iterations finished qdiffx linear iterations at : 13:56:01 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.2365883E-04 3.3210754E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 13:56:02 3.360u 0.171s 0:04.10 86.0% 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 13:56:02 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.097407 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): -0.3620000 45.67000 ymin,ymax (A): 35.28100 86.20100 zmin,zma (A): -23.63900 25.02500 x,y,z range (A): 46.03200 50.92001 48.66400 scale (grids/A): 2.097407 object centre (A): 22.65400 60.74100 0.6929998 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 361.0473 centred at (gu) : 89.01839 90.09669 94.23358 assigned negative charge : -359.5475 centred at (gu) : 89.29114 90.68493 94.04900 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20575 grid for indexing accessible points = 1.400000 m= 31952 mr = 58205 m= 5653 mr = 23919 m= 465 mr = 3665 m= 5 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 35366 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17587 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) : 0.6991358 object centre at (A) : 22.65400 60.74100 0.6929998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8702662E-03 1.7195331E-02 midg,1,midg; midg,igrid,midg 9.8506004E-02 -6.4511962E-02 1,midg,midg; igrid,midg,midg 7.6528807E-04 -8.5475547E-03 gauss-seidel spectral radius is 0.9988416 estimated iterations to convergence 233 setup time was (sec) 0.8700000 now iterating at: 13:56:03 rms-change max change #iterations 4.952053 232.1139 at 10iterations 2.450550 74.61543 at 20iterations 1.220235 40.08015 at 30iterations 0.6062366 16.63291 at 40iterations 0.3021522 9.193111 at 50iterations 0.1503604 4.399124 at 60iterations 7.4913226E-02 2.610391 at 70iterations 3.7431069E-02 1.050198 at 80iterations 1.8806832E-02 0.5228729 at 90iterations 9.5445644E-03 0.2859192 at 100iterations 4.8720487E-03 0.1349373 at 110iterations 2.5833838E-03 8.4104538E-02 at 120iterations finished qdiffx linear iterations at : 13:56:09 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 2.5833838E-03 8.4104538E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 13:56:10 7.532u 0.204s 0:08.19 94.3% 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 13:56:13 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.146111 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): -0.3620000 45.67000 ymin,ymax (A): 35.28100 86.20100 zmin,zma (A): -23.63900 25.02500 x,y,z range (A): 46.03200 50.92001 48.66400 scale (grids/A): 3.146111 object centre (A): 22.65400 60.74100 0.6929998 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500019 assigned positive charge : 361.0473 centred at (gu) : 88.52757 90.14494 96.35033 assigned negative charge : -359.5475 centred at (gu) : 88.93661 91.02731 96.07336 start vw surface at 0.1700000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 191854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20575 grid for indexing accessible points = 1.400000 m= 101349 mr = 140348 m= 39446 mr = 83607 m= 10518 mr = 32106 m= 1872 mr = 8028 m= 176 mr = 1337 m= 8 mr = 103 m= 0 mr = 3 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.970000 number of dielectric boundary points 79691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 17736 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) : 2.097407 object centre at (A) : 22.65400 60.74100 0.6929998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2124583 0.4090734 midg,1,midg; midg,igrid,midg 1.614819 -0.7280121 1,midg,midg; igrid,midg,midg -6.0827810E-02 -2.9443532E-02 gauss-seidel spectral radius is 0.9993036 estimated iterations to convergence 299 setup time was (sec) 2.270000 now iterating at: 13:56:15 rms-change max change #iterations 11.05673 367.6484 at 10iterations 6.565409 151.6260 at 20iterations 3.880413 85.13175 at 30iterations 2.293804 40.67165 at 40iterations 1.355965 23.43102 at 50iterations 0.7993708 13.48532 at 60iterations 0.4709910 8.352627 at 70iterations 0.2768864 5.267885 at 80iterations 0.1624025 2.788383 at 90iterations 9.5491067E-02 1.627218 at 100iterations 5.6233410E-02 0.9460545 at 110iterations 3.3235803E-02 0.5576630 at 120iterations 1.9755173E-02 0.3449459 at 130iterations 1.1903008E-02 0.1964912 at 140iterations 7.3649222E-03 0.1427536 at 150iterations 4.7350978E-03 9.6282959E-02 at 160iterations 3.2230958E-03 7.2246552E-02 at 170iterations 2.3368774E-03 4.9007416E-02 at 180iterations finished qdiffx linear iterations at : 13:56:25 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 2.3368774E-03 4.9007416E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 13:56:26 12.776u 0.223s 0:13.49 96.2% 0+0k 0+0io 0pf+0w