Tue Oct 11 06:33:02 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 Tue Oct 11 2011 at 06:33:02 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7246230 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): -40.97800 -1.171000 ymin,ymax (A): -26.98100 18.72200 zmin,zma (A): -15.02400 34.10500 x,y,z range (A): 39.80700 45.70300 49.12900 scale (grids/A): 0.7246230 object centre (A): -21.07450 -4.129499 9.540500 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.5081 centred at (gu) : 91.26347 89.70272 89.19851 assigned negative charge : -311.5631 centred at (gu) : 91.30804 89.83502 89.16640 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7474 nv = 96 ne = 84 npr = 41374 no. pairs analyzed = 41374 no. exposed pairs = 2480 no. arc points = 17035 no. surface atoms = 845 nbur = 1227 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 507 mr = 4328 m= 4 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1534 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8024 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9784654E-08 8.4280373E-08 midg,1,midg; midg,igrid,midg 1.7825235E-07 -1.9714232E-08 1,midg,midg; igrid,midg,midg 8.4338872E-08 5.3446154E-08 gauss-seidel spectral radius is 0.9900680 estimated iterations to convergence 82 setup time was (sec) 0.3500000 now iterating at: 06:33:02 rms-change max change #iterations 0.2293148 31.44582 at 10iterations 3.0011928E-02 4.229652 at 20iterations 3.9685280E-03 0.4977341 at 30iterations 6.4531429E-04 7.7808380E-02 at 40iterations 1.4471459E-04 1.8869400E-02 at 50iterations finished qdiffx linear iterations at : 06:33:05 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.4471459E-04 1.8869400E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:33:06 3.317u 0.174s 0:03.98 87.4% 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 Tue Oct 11 2011 at 06:33:06 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.173869 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): -40.97800 -1.171000 ymin,ymax (A): -26.98100 18.72200 zmin,zma (A): -15.02400 34.10500 x,y,z range (A): 39.80700 45.70300 49.12900 scale (grids/A): 2.173869 object centre (A): -21.07450 -4.129499 9.540500 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.5081 centred at (gu) : 93.79056 89.10815 87.59554 assigned negative charge : -311.5631 centred at (gu) : 93.92418 89.50526 87.49911 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17035 grid for indexing accessible points = 1.400000 m= 32196 mr = 56306 m= 6548 mr = 24696 m= 632 mr = 4452 m= 17 mr = 337 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 32414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15421 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) : 0.7246230 object centre at (A) : -21.07450 -4.129499 9.540500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1274358E-02 3.1661980E-02 midg,1,midg; midg,igrid,midg 5.8836337E-02 1.6530428E-02 1,midg,midg; igrid,midg,midg 1.8754749E-02 3.6163643E-02 gauss-seidel spectral radius is 0.9988777 estimated iterations to convergence 236 setup time was (sec) 0.6200000 now iterating at: 06:33:07 rms-change max change #iterations 4.868942 197.6442 at 10iterations 2.443676 98.99271 at 20iterations 1.240159 37.35032 at 30iterations 0.6234689 18.39268 at 40iterations 0.3137945 10.45811 at 50iterations 0.1584848 4.571688 at 60iterations 7.9849444E-02 2.257807 at 70iterations 4.0286601E-02 1.177151 at 80iterations 2.0359455E-02 0.5981750 at 90iterations 1.0341396E-02 0.3822784 at 100iterations 5.2550994E-03 0.1528339 at 110iterations 2.6839511E-03 7.6368332E-02 at 120iterations finished qdiffx linear iterations at : 06:33:14 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.6839511E-03 7.6368332E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 06:33:14 7.769u 0.194s 0:08.30 95.7% 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 Tue Oct 11 2011 at 06:33:14 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.260803 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): -40.97800 -1.171000 ymin,ymax (A): -26.98100 18.72200 zmin,zma (A): -15.02400 34.10500 x,y,z range (A): 39.80700 45.70300 49.12900 scale (grids/A): 3.260803 object centre (A): -21.07450 -4.129499 9.540500 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.5081 centred at (gu) : 95.68581 88.66225 86.39327 assigned negative charge : -311.5631 centred at (gu) : 95.88641 89.25785 86.24876 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 181655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17035 grid for indexing accessible points = 1.400000 m= 99988 mr = 135504 m= 41628 mr = 83628 m= 12407 mr = 34532 m= 2539 mr = 9696 m= 314 mr = 1874 m= 17 mr = 237 m= 0 mr = 2 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 73075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 15504 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) : 2.173869 object centre at (A) : -21.07450 -4.129499 9.540500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3273447 0.1711366 midg,1,midg; midg,igrid,midg 0.4730536 0.1603060 1,midg,midg; igrid,midg,midg 0.1268479 0.4110902 gauss-seidel spectral radius is 0.9993090 estimated iterations to convergence 300 setup time was (sec) 1.470000 now iterating at: 06:33:16 rms-change max change #iterations 10.65143 439.2728 at 10iterations 6.322359 149.6407 at 20iterations 3.753270 89.45632 at 30iterations 2.224810 49.60520 at 40iterations 1.318779 23.90494 at 50iterations 0.7778828 15.52670 at 60iterations 0.4588996 8.749147 at 70iterations 0.2708180 5.500365 at 80iterations 0.1596389 2.741150 at 90iterations 9.4128646E-02 1.589050 at 100iterations 5.5645976E-02 1.060757 at 110iterations 3.3049528E-02 0.5456543 at 120iterations 1.9731615E-02 0.3712072 at 130iterations 1.1956728E-02 0.2020569 at 140iterations 7.4705607E-03 0.1296558 at 150iterations 4.8568035E-03 8.0793381E-02 at 160iterations 3.3166877E-03 6.1607361E-02 at 170iterations 2.4084318E-03 4.2655945E-02 at 180iterations finished qdiffx linear iterations at : 06:33:27 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 2.4084318E-03 4.2655945E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 06:33:28 12.916u 0.191s 0:13.50 97.0% 0+0k 0+0io 0pf+0w