Mon Oct 10 17:02:21 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+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 Mon Oct 10 2011 at 17:02:21 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 = 2846 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: 0.6168347 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): -8.905000 48.80900 ymin,ymax (A): -7.930000 38.89900 zmin,zma (A): 0.7129999 55.79700 x,y,z range (A): 57.71400 46.82900 55.08400 scale (grids/A): 0.6168347 object centre (A): 19.95200 15.48450 28.25500 number of atom coordinates read : 2846 total number of charged atoms : 2705 net assigned charge : -2.999972 assigned positive charge : 426.6312 centred at (gu) : 89.23598 89.68225 88.72478 assigned negative charge : -429.6322 centred at (gu) : 89.15467 89.59865 88.68557 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7426 nv = 96 ne = 84 npr = 56347 no. pairs analyzed = 56347 no. exposed pairs = 3763 no. arc points = 26670 no. surface atoms = 1276 nbur = 1570 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3924 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3100000 number of dielectric boundary points 3830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2683 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8952 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2550569E-09 3.7777825E-10 midg,1,midg; midg,igrid,midg -8.2930045E-09 3.2188947E-09 1,midg,midg; igrid,midg,midg -8.9780938E-09 2.7759970E-09 gauss-seidel spectral radius is 0.9864206 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 17:02:22 rms-change max change #iterations 0.1293639 20.79550 at 10iterations 1.1684318E-02 1.674369 at 20iterations 1.0904799E-03 0.1653748 at 30iterations 9.9895289E-05 1.5584946E-02 at 40iterations 9.9158842E-06 1.4375448E-03 at 50iterations finished qdiffx linear iterations at : 17:02:24 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 9.9158842E-06 1.4375448E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 17:02:26 3.087u 0.146s 0:04.31 74.7% 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 Mon Oct 10 2011 at 17:02:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2846 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.850504 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): -8.905000 48.80900 ymin,ymax (A): -7.930000 38.89900 zmin,zma (A): 0.7129999 55.79700 x,y,z range (A): 57.71400 46.82900 55.08400 scale (grids/A): 1.850504 object centre (A): 19.95200 15.48450 28.25500 number of atom coordinates read : 2846 total number of charged atoms : 2705 net assigned charge : -2.999972 assigned positive charge : 426.6312 centred at (gu) : 87.70696 89.04601 86.17330 assigned negative charge : -429.6322 centred at (gu) : 87.46349 88.79588 86.05643 start vw surface at 0.2500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 79890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26670 grid for indexing accessible points = 1.400000 m= 27450 mr = 54208 m= 3794 mr = 19551 m= 180 mr = 2220 m= 0 mr = 41 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1320 time to turn everything in is 0.6500000 number of dielectric boundary points 35294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21203 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) : 0.6168347 object centre at (A) : 19.95200 15.48450 28.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5861638E-04 3.2550283E-03 midg,1,midg; midg,igrid,midg -2.0561880E-02 -6.7863055E-04 1,midg,midg; igrid,midg,midg -4.8446637E-02 2.3488082E-02 gauss-seidel spectral radius is 0.9985874 estimated iterations to convergence 211 setup time was (sec) 0.9400000 now iterating at: 17:02:27 rms-change max change #iterations 4.235901 195.4117 at 10iterations 1.954354 92.43788 at 20iterations 0.9026042 29.40331 at 30iterations 0.4157004 13.01215 at 40iterations 0.1922006 5.906113 at 50iterations 8.8822819E-02 2.852018 at 60iterations 4.1008495E-02 1.215353 at 70iterations 1.8939070E-02 0.7033068 at 80iterations 8.7683033E-03 0.2822144 at 90iterations 4.0538041E-03 0.1375237 at 100iterations 1.8730746E-03 6.0413361E-02 at 110iterations 8.6483522E-04 2.6691437E-02 at 120iterations finished qdiffx linear iterations at : 17:02:33 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 8.6483522E-04 2.6691437E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 17:02:33 7.116u 0.193s 0:07.62 95.8% 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 17:02:33 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 = 2846 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: 2.775756 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): -8.905000 48.80900 ymin,ymax (A): -7.930000 38.89900 zmin,zma (A): 0.7129999 55.79700 x,y,z range (A): 57.71400 46.82900 55.08400 scale (grids/A): 2.775756 object centre (A): 19.95200 15.48450 28.25500 number of atom coordinates read : 2846 total number of charged atoms : 2705 net assigned charge : -2.999972 assigned positive charge : 426.6312 centred at (gu) : 86.56014 88.56889 84.25983 assigned negative charge : -429.6322 centred at (gu) : 86.19536 88.19373 84.08456 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 184989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26670 grid for indexing accessible points = 1.400000 m= 90150 mr = 132049 m= 30511 mr = 72454 m= 6515 mr = 23747 m= 764 mr = 4701 m= 31 mr = 424 m= 0 mr = 12 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 4343 time to turn everything in is 1.380000 number of dielectric boundary points 79573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 21638 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) : 1.850504 object centre at (A) : 19.95200 15.48450 28.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6484534E-02 -0.1778502 midg,1,midg; midg,igrid,midg -0.1910751 -2.2799725E-02 1,midg,midg; igrid,midg,midg -0.6447691 0.3571030 gauss-seidel spectral radius is 0.9992658 estimated iterations to convergence 291 setup time was (sec) 1.700000 now iterating at: 17:02:35 rms-change max change #iterations 10.28209 334.0533 at 10iterations 6.097367 183.5916 at 20iterations 3.580306 93.51150 at 30iterations 2.090574 47.92030 at 40iterations 1.217386 25.24579 at 50iterations 0.7077101 14.38864 at 60iterations 0.4111356 8.637690 at 70iterations 0.2378056 5.199368 at 80iterations 0.1376672 2.783089 at 90iterations 7.9628937E-02 1.497177 at 100iterations 4.5994271E-02 0.8475924 at 110iterations 2.6534118E-02 0.5162735 at 120iterations 1.5282332E-02 0.2844968 at 130iterations 8.8274600E-03 0.1711745 at 140iterations 5.0975154E-03 8.9920044E-02 at 150iterations 2.9334363E-03 5.0817490E-02 at 160iterations 1.6935631E-03 3.1127930E-02 at 170iterations 9.7638811E-04 1.9347668E-02 at 180iterations finished qdiffx linear iterations at : 17:02:46 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 9.7638811E-04 1.9347668E-02 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 17:02:46 12.275u 0.188s 0:12.81 97.1% 0+0k 0+0io 0pf+0w