Tue Oct 11 03:36:05 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 03:36:05 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2187 !!! WARNING: HIR 435 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6390006 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): -45.88700 8.027000 ymin,ymax (A): -38.31400 5.712000 zmin,zma (A): -50.59500 5.117000 x,y,z range (A): 53.91400 44.02600 55.71200 scale (grids/A): 0.6390006 object centre (A): -18.93000 -16.30100 -22.73900 number of atom coordinates read : 2187 total number of charged atoms : 2077 net assigned charge : -5.485982 assigned positive charge : 322.0984 centred at (gu) : 90.43561 90.56745 90.07942 assigned negative charge : -327.5848 centred at (gu) : 90.28600 90.62099 90.07863 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6041 nv = 96 ne = 84 npr = 45172 no. pairs analyzed = 45172 no. exposed pairs = 2717 no. arc points = 19254 no. surface atoms = 923 nbur = 1264 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3300 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3100000 number of dielectric boundary points 3025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1772 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7187 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7323818E-09 -7.8359266E-09 midg,1,midg; midg,igrid,midg -2.4174587E-09 -1.4601842E-08 1,midg,midg; igrid,midg,midg -2.0367862E-08 6.9972188E-09 gauss-seidel spectral radius is 0.9872789 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 03:36:06 rms-change max change #iterations 0.1307935 20.92529 at 10iterations 1.2818739E-02 2.185898 at 20iterations 1.2718129E-03 0.1842785 at 30iterations 1.2566368E-04 1.8037796E-02 at 40iterations 1.2273435E-05 1.8653870E-03 at 50iterations finished qdiffx linear iterations at : 03:36:09 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.2273435E-05 1.8653870E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 03:36:10 4.036u 0.246s 0:04.87 87.6% 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 Tue Oct 11 2011 at 03:36:10 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2187 !!! WARNING: HIR 435 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.917002 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): -45.88700 8.027000 ymin,ymax (A): -38.31400 5.712000 zmin,zma (A): -50.59500 5.117000 x,y,z range (A): 53.91400 44.02600 55.71200 scale (grids/A): 1.917002 object centre (A): -18.93000 -16.30100 -22.73900 number of atom coordinates read : 2187 total number of charged atoms : 2077 net assigned charge : -5.485982 assigned positive charge : 322.0984 centred at (gu) : 91.30650 91.70189 90.23804 assigned negative charge : -327.5848 centred at (gu) : 90.85798 91.86296 90.23578 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 65328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19254 grid for indexing accessible points = 1.400000 m= 23080 mr = 45080 m= 3494 mr = 16855 m= 156 mr = 2144 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 581 time to turn everything in is 0.6000000 number of dielectric boundary points 27939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 16342 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) : 0.6390006 object centre at (A) : -18.93000 -16.30100 -22.73900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2620288E-02 -7.4798020E-04 midg,1,midg; midg,igrid,midg 7.2018737E-03 6.3198647E-03 1,midg,midg; igrid,midg,midg -7.4063212E-02 -3.7380498E-02 gauss-seidel spectral radius is 0.9986138 estimated iterations to convergence 213 setup time was (sec) 0.9000000 now iterating at: 03:36:11 rms-change max change #iterations 3.891610 186.2239 at 10iterations 1.816520 67.32516 at 20iterations 0.8432124 28.67144 at 30iterations 0.3922335 14.56675 at 40iterations 0.1824171 6.210979 at 50iterations 8.5019901E-02 2.851584 at 60iterations 3.9540343E-02 1.325178 at 70iterations 1.8455923E-02 0.5964622 at 80iterations 8.5659642E-03 0.2919569 at 90iterations 4.0016761E-03 0.1328506 at 100iterations 1.8602277E-03 7.2170258E-02 at 110iterations 8.6648570E-04 2.9117584E-02 at 120iterations finished qdiffx linear iterations at : 03:36:19 total time elapsed so far: 9.070000 # loops : 120 mean,max change (kT/e) : 8.6648570E-04 2.9117584E-02 energy calculations done at 9.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.250000 DelPhi exited at 03:36:21 9.249u 0.279s 0:11.21 84.8% 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 Tue Oct 11 2011 at 03:36:21 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2187 !!! WARNING: HIR 435 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.875503 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): -45.88700 8.027000 ymin,ymax (A): -38.31400 5.712000 zmin,zma (A): -50.59500 5.117000 x,y,z range (A): 53.91400 44.02600 55.71200 scale (grids/A): 2.875503 object centre (A): -18.93000 -16.30100 -22.73900 number of atom coordinates read : 2187 total number of charged atoms : 2077 net assigned charge : -5.485982 assigned positive charge : 322.0984 centred at (gu) : 91.95970 92.55278 90.35688 assigned negative charge : -327.5848 centred at (gu) : 91.28692 92.79441 90.35371 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 151236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19254 grid for indexing accessible points = 1.400000 m= 74784 mr = 109147 m= 26729 mr = 61067 m= 6223 mr = 21470 m= 786 mr = 4645 m= 24 mr = 483 m= 0 mr = 6 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1921 time to turn everything in is 1.500000 number of dielectric boundary points 62964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 16614 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) : 1.917002 object centre at (A) : -18.93000 -16.30100 -22.73900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3340101 -4.3096516E-02 midg,1,midg; midg,igrid,midg 8.0035642E-02 8.3093368E-02 1,midg,midg; igrid,midg,midg -0.8545167 -0.2910168 gauss-seidel spectral radius is 0.9992507 estimated iterations to convergence 288 setup time was (sec) 1.810000 now iterating at: 03:36:23 rms-change max change #iterations 9.032758 351.8502 at 10iterations 5.196852 133.8741 at 20iterations 2.982333 63.28712 at 30iterations 1.707859 34.35966 at 40iterations 0.9741372 21.01562 at 50iterations 0.5563232 12.96781 at 60iterations 0.3186044 5.829189 at 70iterations 0.1819033 3.321632 at 80iterations 0.1039595 1.975960 at 90iterations 5.9327424E-02 1.238312 at 100iterations 3.3839438E-02 0.6401253 at 110iterations 1.9329511E-02 0.3833494 at 120iterations 1.1054759E-02 0.2220650 at 130iterations 6.3203010E-03 0.1203073 at 140iterations 3.6116007E-03 7.0552826E-02 at 150iterations 2.0634825E-03 4.7920227E-02 at 160iterations 1.1780994E-03 2.2202730E-02 at 170iterations 6.7382323E-04 1.2365341E-02 at 180iterations finished qdiffx linear iterations at : 03:36:37 total time elapsed so far: 15.09000 # loops : 180 mean,max change (kT/e) : 6.7382323E-04 1.2365341E-02 energy calculations done at 15.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.26000 DelPhi exited at 03:36:38 15.266u 0.311s 0:16.40 94.9% 0+0k 0+0io 0pf+0w