Tue Oct 11 06:04:43 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 06:04:43 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 0.7359478 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): -9.108000 35.03500 ymin,ymax (A): -3.635000 34.14500 zmin,zma (A): 1.179000 49.55200 x,y,z range (A): 44.14300 37.77999 48.37300 scale (grids/A): 0.7359478 object centre (A): 12.96350 15.25500 25.36550 number of atom coordinates read : 2010 total number of charged atoms : 1885 net assigned charge : 5.931007 assigned positive charge : 305.2772 centred at (gu) : 90.16685 89.52702 91.41756 assigned negative charge : -299.3462 centred at (gu) : 89.98008 89.58217 91.47655 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7635 nv = 96 ne = 84 npr = 39972 no. pairs analyzed = 39972 no. exposed pairs = 2468 no. arc points = 16756 no. surface atoms = 840 nbur = 1170 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 568 mr = 4487 m= 7 mr = 111 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 0.2700000 number of dielectric boundary points 3612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1491 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8024 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1344739E-07 5.6125824E-08 midg,1,midg; midg,igrid,midg 1.5705542E-07 4.3958458E-08 1,midg,midg; igrid,midg,midg -6.7568621E-08 2.6426164E-07 gauss-seidel spectral radius is 0.9903646 estimated iterations to convergence 83 setup time was (sec) 0.5000000 now iterating at: 06:04:43 rms-change max change #iterations 0.2340682 31.62645 at 10iterations 3.1587668E-02 4.037457 at 20iterations 4.2991745E-03 0.6712074 at 30iterations 6.4692792E-04 0.1057892 at 40iterations 1.3584425E-04 1.6708374E-02 at 50iterations finished qdiffx linear iterations at : 06:04:46 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.3584425E-04 1.6708374E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 06:04:47 3.486u 0.158s 0:04.21 86.2% 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 06:04:47 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 2.207843 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): -9.108000 35.03500 ymin,ymax (A): -3.635000 34.14500 zmin,zma (A): 1.179000 49.55200 x,y,z range (A): 44.14300 37.77999 48.37300 scale (grids/A): 2.207843 object centre (A): 12.96350 15.25500 25.36550 number of atom coordinates read : 2010 total number of charged atoms : 1885 net assigned charge : 5.931007 assigned positive charge : 305.2772 centred at (gu) : 90.50063 88.58110 94.25253 assigned negative charge : -299.3462 centred at (gu) : 89.94035 88.74656 94.42989 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16756 grid for indexing accessible points = 1.400000 m= 34177 mr = 57315 m= 7353 mr = 26553 m= 805 mr = 5055 m= 23 mr = 462 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 32933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15023 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) : 0.7359478 object centre at (A) : 12.96350 15.25500 25.36550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2067917E-02 1.9090248E-02 midg,1,midg; midg,igrid,midg 3.6243685E-02 7.6948507E-03 1,midg,midg; igrid,midg,midg 2.7952010E-02 6.1352156E-02 gauss-seidel spectral radius is 0.9989039 estimated iterations to convergence 239 setup time was (sec) 0.9100000 now iterating at: 06:04:48 rms-change max change #iterations 4.836294 227.8666 at 10iterations 2.450817 72.01286 at 20iterations 1.247506 37.42457 at 30iterations 0.6352925 20.04477 at 40iterations 0.3229944 8.785693 at 50iterations 0.1646605 4.977980 at 60iterations 8.3675154E-02 2.382559 at 70iterations 4.2523943E-02 1.165442 at 80iterations 2.1708662E-02 0.6081136 at 90iterations 1.1108723E-02 0.3134756 at 100iterations 5.7278774E-03 0.1745911 at 110iterations 2.9807973E-03 8.6610794E-02 at 120iterations finished qdiffx linear iterations at : 06:04:55 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 2.9807973E-03 8.6610794E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 06:04:56 8.102u 0.224s 0:08.88 93.6% 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 06:04:56 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 3.311765 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): -9.108000 35.03500 ymin,ymax (A): -3.635000 34.14500 zmin,zma (A): 1.179000 49.55200 x,y,z range (A): 44.14300 37.77999 48.37300 scale (grids/A): 3.311765 object centre (A): 12.96350 15.25500 25.36550 number of atom coordinates read : 2010 total number of charged atoms : 1885 net assigned charge : 5.931007 assigned positive charge : 305.2772 centred at (gu) : 90.75094 87.87160 96.37879 assigned negative charge : -299.3462 centred at (gu) : 89.91056 88.11991 96.64479 start vw surface at 0.1600000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 183958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16756 grid for indexing accessible points = 1.400000 m= 104209 mr = 137323 m= 45515 mr = 87883 m= 14364 mr = 38083 m= 3170 mr = 11337 m= 451 mr = 2377 m= 11 mr = 322 m= 0 mr = 3 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 74350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 15080 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) : 2.207843 object centre at (A) : 12.96350 15.25500 25.36550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3690826 8.7191172E-02 midg,1,midg; midg,igrid,midg 0.3089792 5.6353197E-02 1,midg,midg; igrid,midg,midg 0.4492404 0.4744354 gauss-seidel spectral radius is 0.9993145 estimated iterations to convergence 301 setup time was (sec) 2.450000 now iterating at: 06:04:59 rms-change max change #iterations 10.56735 258.4916 at 10iterations 6.308818 133.6813 at 20iterations 3.764722 67.51164 at 30iterations 2.242816 42.60542 at 40iterations 1.329151 23.18510 at 50iterations 0.7850329 14.90622 at 60iterations 0.4658074 9.013235 at 70iterations 0.2745020 4.770653 at 80iterations 0.1624206 2.826411 at 90iterations 9.5673785E-02 1.641819 at 100iterations 5.6638747E-02 0.9692187 at 110iterations 3.3451673E-02 0.5794441 at 120iterations 1.9911014E-02 0.3413932 at 130iterations 1.1924577E-02 0.2097554 at 140iterations 7.2569400E-03 0.1414661 at 150iterations 4.5376527E-03 7.0266724E-02 at 160iterations 2.9520278E-03 4.8049927E-02 at 170iterations 2.0370388E-03 3.2768250E-02 at 180iterations finished qdiffx linear iterations at : 06:05:11 total time elapsed so far: 15.15000 # loops : 180 mean,max change (kT/e) : 2.0370388E-03 3.2768250E-02 energy calculations done at 15.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.34000 DelPhi exited at 06:05:12 15.338u 0.286s 0:16.03 97.3% 0+0k 0+0io 0pf+0w