Sun Oct 9 23:11:53 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 Sun Oct 9 2011 at 23:11:53 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 = 3763 !!! WARNING: CYS 258 has a net charge of 0.5000 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: 0.5781285 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): -30.96300 20.77600 ymin,ymax (A): -34.38600 27.19200 zmin,zma (A): -49.59800 4.852000 x,y,z range (A): 51.73900 61.57800 54.45000 scale (grids/A): 0.5781285 object centre (A): -5.093501 -3.597001 -22.37300 number of atom coordinates read : 3763 total number of charged atoms : 3608 net assigned charge : 2.500001 assigned positive charge : 566.0656 centred at (gu) : 90.28738 90.61172 89.83529 assigned negative charge : -563.5685 centred at (gu) : 90.19099 90.55057 89.63974 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8549 nv = 96 ne = 84 npr = 72985 no. pairs analyzed = 72985 no. exposed pairs = 4944 no. arc points = 34699 no. surface atoms = 1656 nbur = 2107 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 406 mr = 4571 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3410 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9355360E-09 5.3095914E-09 midg,1,midg; midg,igrid,midg -9.5383768E-10 2.4300852E-09 1,midg,midg; igrid,midg,midg -1.9118049E-09 3.2218124E-09 gauss-seidel spectral radius is 0.9846309 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 23:11:54 rms-change max change #iterations 0.1119656 16.27740 at 10iterations 8.6846659E-03 1.292411 at 20iterations 6.8952888E-04 8.5548401E-02 at 30iterations 6.0900442E-05 7.7705383E-03 at 40iterations 1.0242085E-05 1.7056465E-03 at 50iterations finished qdiffx linear iterations at : 23:11:56 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 1.0242085E-05 1.7056465E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 23:11:57 3.146u 0.164s 0:03.72 88.7% 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 Sun Oct 9 2011 at 23:11:57 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 = 3763 !!! WARNING: CYS 258 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.734386 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): -30.96300 20.77600 ymin,ymax (A): -34.38600 27.19200 zmin,zma (A): -49.59800 4.852000 x,y,z range (A): 51.73900 61.57800 54.45000 scale (grids/A): 1.734386 object centre (A): -5.093501 -3.597001 -22.37300 number of atom coordinates read : 3763 total number of charged atoms : 3608 net assigned charge : 2.500001 assigned positive charge : 566.0656 centred at (gu) : 90.86080 91.83382 89.50481 assigned negative charge : -563.5685 centred at (gu) : 90.57261 91.65113 88.91872 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 94310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34699 grid for indexing accessible points = 1.400000 m= 32622 mr = 65109 m= 4192 mr = 23245 m= 169 mr = 2366 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 273 time to turn everything in is 0.6500000 number of dielectric boundary points 40515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 27988 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) : 0.5781285 object centre at (A) : -5.093501 -3.597001 -22.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3651490E-02 1.4778620E-02 midg,1,midg; midg,igrid,midg 2.0109011E-02 1.5209691E-02 1,midg,midg; igrid,midg,midg -1.6880436E-02 1.3619950E-03 gauss-seidel spectral radius is 0.9984893 estimated iterations to convergence 204 setup time was (sec) 0.9200000 now iterating at: 23:11:58 rms-change max change #iterations 4.330195 184.2992 at 10iterations 1.940050 71.54494 at 20iterations 0.8701332 25.77103 at 30iterations 0.3928345 14.01152 at 40iterations 0.1762379 5.919724 at 50iterations 7.9228386E-02 2.481834 at 60iterations 3.5577133E-02 1.113903 at 70iterations 1.6022373E-02 0.4812126 at 80iterations 7.2404225E-03 0.2171249 at 90iterations 3.2719004E-03 0.1039691 at 100iterations 1.4815105E-03 4.4407845E-02 at 110iterations 6.7218282E-04 1.8878937E-02 at 120iterations finished qdiffx linear iterations at : 23:12:04 total time elapsed so far: 7.090000 # loops : 120 mean,max change (kT/e) : 6.7218282E-04 1.8878937E-02 energy calculations done at 7.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.270000 DelPhi exited at 23:12:05 7.269u 0.172s 0:07.76 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 Sun Oct 9 2011 at 23:12:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3763 !!! WARNING: CYS 258 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.601578 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): -30.96300 20.77600 ymin,ymax (A): -34.38600 27.19200 zmin,zma (A): -49.59800 4.852000 x,y,z range (A): 51.73900 61.57800 54.45000 scale (grids/A): 2.601578 object centre (A): -5.093501 -3.597001 -22.37300 number of atom coordinates read : 3763 total number of charged atoms : 3608 net assigned charge : 2.500001 assigned positive charge : 566.0656 centred at (gu) : 91.29100 92.75043 89.25695 assigned negative charge : -563.5685 centred at (gu) : 90.85875 92.47660 88.37787 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 218508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34699 grid for indexing accessible points = 1.400000 m= 109400 mr = 158624 m= 35257 mr = 87990 m= 7109 mr = 27358 m= 812 mr = 5106 m= 31 mr = 511 m= 0 mr = 6 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 961 time to turn everything in is 1.570000 number of dielectric boundary points 91522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 28849 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) : 1.734386 object centre at (A) : -5.093501 -3.597001 -22.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3735838 0.1527437 midg,1,midg; midg,igrid,midg 9.7208731E-02 0.3445632 1,midg,midg; igrid,midg,midg -0.1824586 -1.3758846E-02 gauss-seidel spectral radius is 0.9992552 estimated iterations to convergence 289 setup time was (sec) 1.850000 now iterating at: 23:12:07 rms-change max change #iterations 10.94944 293.2652 at 10iterations 6.524044 150.0307 at 20iterations 3.848232 84.08750 at 30iterations 2.260618 56.11909 at 40iterations 1.318566 29.03911 at 50iterations 0.7674843 16.87771 at 60iterations 0.4457006 8.673172 at 70iterations 0.2581652 4.939236 at 80iterations 0.1491293 2.889698 at 90iterations 8.5965030E-02 1.482135 at 100iterations 4.9672164E-02 1.036623 at 110iterations 2.8628001E-02 0.5160503 at 120iterations 1.6510800E-02 0.2915688 at 130iterations 9.4939703E-03 0.1560636 at 140iterations 5.4616570E-03 9.1052771E-02 at 150iterations 3.1513521E-03 5.3804398E-02 at 160iterations 1.8183115E-03 3.3287048E-02 at 170iterations 1.0542307E-03 1.8253326E-02 at 180iterations finished qdiffx linear iterations at : 23:12:16 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 1.0542307E-03 1.8253326E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 23:12:17 11.517u 0.160s 0:11.98 97.4% 0+0k 0+0io 0pf+0w