Sat Oct 15 14:55:34 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 Sat Oct 15 2011 at 14:55:35 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4143 !!! WARNING: HIZ 82 has a net charge of 0.2000 !!! WARNING: HIZ 118 has a net charge of 0.2000 !!! WARNING: GLM 282 has a net charge of -0.0940 !!! WARNING: HIZ 442 has a net charge of 0.2000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: ZN1 1303 has a net charge of 1.4000 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: 0.4981041 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): -44.70900 26.76200 ymin,ymax (A): -62.10500 3.317000 zmin,zma (A): 11.72900 71.16600 x,y,z range (A): 71.47100 65.42200 59.43700 scale (grids/A): 0.4981041 object centre (A): -8.973499 -29.39400 41.44750 number of atom coordinates read : 4143 total number of charged atoms : 3986 net assigned charge : 6.806046 assigned positive charge : 642.5323 centred at (gu) : 89.33464 89.95625 88.36481 assigned negative charge : -635.7302 centred at (gu) : 89.38986 89.84113 88.45694 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6700 nv = 96 ne = 84 npr = 77518 no. pairs analyzed = 77518 no. exposed pairs = 5969 no. arc points = 43324 no. surface atoms = 1969 nbur = 2174 mkacc time = 0.1300000 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 = 1.708000 m= 259 mr = 2940 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 4017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4219 ## 723 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9054 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7011418E-10 -4.5818526E-11 midg,1,midg; midg,igrid,midg -1.0521118E-10 2.0029101E-10 1,midg,midg; igrid,midg,midg 1.4928331E-10 -1.8240090E-11 gauss-seidel spectral radius is 0.9793718 estimated iterations to convergence 58 setup time was (sec) 0.5200000 now iterating at: 14:55:35 rms-change max change #iterations 5.3847026E-02 12.83899 at 10iterations 2.9585480E-03 0.4698887 at 20iterations 2.8947840E-04 4.9064636E-02 at 30iterations 5.7288213E-05 9.7970963E-03 at 40iterations 1.2705918E-05 2.0780563E-03 at 50iterations finished qdiffx linear iterations at : 14:55:39 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.2705918E-05 2.0780563E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 14:55:39 3.976u 0.218s 0:04.49 93.0% 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 Sat Oct 15 2011 at 14:55:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4143 !!! WARNING: HIZ 82 has a net charge of 0.2000 !!! WARNING: HIZ 118 has a net charge of 0.2000 !!! WARNING: GLM 282 has a net charge of -0.0940 !!! WARNING: HIZ 442 has a net charge of 0.2000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: ZN1 1303 has a net charge of 1.4000 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: 1.494312 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): -44.70900 26.76200 ymin,ymax (A): -62.10500 3.317000 zmin,zma (A): 11.72900 71.16600 x,y,z range (A): 71.47100 65.42200 59.43700 scale (grids/A): 1.494312 object centre (A): -8.973499 -29.39400 41.44750 number of atom coordinates read : 4143 total number of charged atoms : 3986 net assigned charge : 6.806046 assigned positive charge : 642.5323 centred at (gu) : 88.00286 89.86741 85.09317 assigned negative charge : -635.7302 centred at (gu) : 88.16934 89.52347 85.37051 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 74826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43324 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 20703 mr = 46391 m= 1765 mr = 12784 m= 27 mr = 655 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 37491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 628 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 29701 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) : 0.4981041 object centre at (A) : -8.973499 -29.39400 41.44750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3506885E-02 -3.4345449E-03 midg,1,midg; midg,igrid,midg 1.0468421E-03 2.6345595E-03 1,midg,midg; igrid,midg,midg 6.5168384E-03 -1.0368832E-02 gauss-seidel spectral radius is 0.9979655 estimated iterations to convergence 176 setup time was (sec) 0.6700000 now iterating at: 14:55:40 rms-change max change #iterations 3.343133 147.3887 at 10iterations 1.317391 60.53711 at 20iterations 0.5192516 20.09194 at 30iterations 0.2047585 7.286819 at 40iterations 8.0896720E-02 2.838464 at 50iterations 3.1977475E-02 1.259167 at 60iterations 1.2625626E-02 0.4343653 at 70iterations 5.0060460E-03 0.2064047 at 80iterations 1.9893828E-03 8.6399317E-02 at 90iterations 7.9506828E-04 2.9046297E-02 at 100iterations 3.1910883E-04 1.1455536E-02 at 110iterations 1.3111233E-04 4.5442581E-03 at 120iterations finished qdiffx linear iterations at : 14:55:48 total time elapsed so far: 8.890000 # loops : 120 mean,max change (kT/e) : 1.3111233E-04 4.5442581E-03 energy calculations done at 8.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.020000 DelPhi exited at 14:55:49 9.027u 0.264s 0:09.76 95.0% 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 Sat Oct 15 2011 at 14:55:49 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4143 !!! WARNING: HIZ 82 has a net charge of 0.2000 !!! WARNING: HIZ 118 has a net charge of 0.2000 !!! WARNING: GLM 282 has a net charge of -0.0940 !!! WARNING: HIZ 442 has a net charge of 0.2000 !!! WARNING: MG1 1299 has a net charge of 1.4000 !!! WARNING: ZN1 1303 has a net charge of 1.4000 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: 2.241468 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): -44.70900 26.76200 ymin,ymax (A): -62.10500 3.317000 zmin,zma (A): 11.72900 71.16600 x,y,z range (A): 71.47100 65.42200 59.43700 scale (grids/A): 2.241468 object centre (A): -8.973499 -29.39400 41.44750 number of atom coordinates read : 4143 total number of charged atoms : 3986 net assigned charge : 6.806046 assigned positive charge : 642.5323 centred at (gu) : 87.00399 89.80057 82.63938 assigned negative charge : -635.7302 centred at (gu) : 87.25402 89.28497 83.05578 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 174169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43324 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 73003 mr = 115640 m= 18544 mr = 53885 m= 2296 mr = 12695 m= 81 mr = 1301 m= 0 mr = 23 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 84549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 31760 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) : 1.494312 object centre at (A) : -8.973499 -29.39400 41.44750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2870381 -6.1248381E-02 midg,1,midg; midg,igrid,midg 2.2536989E-02 -0.1708557 1,midg,midg; igrid,midg,midg 0.1072975 -0.1673344 gauss-seidel spectral radius is 0.9991074 estimated iterations to convergence 264 setup time was (sec) 1.230000 now iterating at: 14:55:50 rms-change max change #iterations 9.411040 259.4260 at 10iterations 5.369130 144.3593 at 20iterations 3.010327 87.23517 at 30iterations 1.677864 39.50225 at 40iterations 0.9310470 24.81848 at 50iterations 0.5144903 12.91445 at 60iterations 0.2828117 6.881377 at 70iterations 0.1549709 3.940996 at 80iterations 8.4841281E-02 1.872280 at 90iterations 4.6355490E-02 1.017334 at 100iterations 2.5326371E-02 0.5323029 at 110iterations 1.3809174E-02 0.3042135 at 120iterations 7.5262729E-03 0.1634684 at 130iterations 4.0967902E-03 8.8055611E-02 at 140iterations 2.2339593E-03 4.6285629E-02 at 150iterations 1.2160417E-03 2.5110245E-02 at 160iterations 6.6190516E-04 1.5123367E-02 at 170iterations 3.6137013E-04 7.8315735E-03 at 180iterations finished qdiffx linear iterations at : 14:56:04 total time elapsed so far: 14.78000 # loops : 180 mean,max change (kT/e) : 3.6137013E-04 7.8315735E-03 energy calculations done at 14.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.92000 DelPhi exited at 14:56:04 14.922u 0.297s 0:15.59 97.5% 0+0k 0+0io 0pf+0w