Sun Oct 9 15:23:36 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 Sun Oct 9 2011 at 15:23:36 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5365 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: 0.5009288 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): 67.46900 138.5370 ymin,ymax (A): -6.225000 57.14200 zmin,zma (A): -3.372000 63.71800 x,y,z range (A): 71.06799 63.36700 67.09000 scale (grids/A): 0.5009288 object centre (A): 103.0030 25.45850 30.17300 number of atom coordinates read : 5365 total number of charged atoms : 5195 net assigned charge : -1.499968 assigned positive charge : 818.9024 centred at (gu) : 89.07233 90.59045 90.50963 assigned negative charge : -820.4093 centred at (gu) : 89.09192 90.52261 90.58128 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8186 nv = 96 ne = 84 npr = 111282 no. pairs analyzed = 111282 no. exposed pairs = 6017 no. arc points = 42089 no. surface atoms = 2019 nbur = 3346 mkacc time = 0.1900000 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= 269 mr = 4490 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3600000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4021 ## 592 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11205 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0831681E-10 -1.7859964E-10 midg,1,midg; midg,igrid,midg -1.2605177E-10 1.3779805E-10 1,midg,midg; igrid,midg,midg 3.1171746E-11 -4.0937385E-11 gauss-seidel spectral radius is 0.9796518 estimated iterations to convergence 58 setup time was (sec) 0.5500000 now iterating at: 15:23:36 rms-change max change #iterations 6.6879705E-02 10.97091 at 10iterations 3.9880741E-03 0.5880184 at 20iterations 4.5578292E-04 6.8954468E-02 at 30iterations 9.8209137E-05 1.6902924E-02 at 40iterations 2.3372098E-05 4.1065216E-03 at 50iterations finished qdiffx linear iterations at : 15:23:39 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 2.3372098E-05 4.1065216E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 15:23:40 3.566u 0.183s 0:04.03 92.8% 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 Sun Oct 9 2011 at 15:23:40 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5365 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: 1.502786 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): 67.46900 138.5370 ymin,ymax (A): -6.225000 57.14200 zmin,zma (A): -3.372000 63.71800 x,y,z range (A): 71.06799 63.36700 67.09000 scale (grids/A): 1.502786 object centre (A): 103.0030 25.45850 30.17300 number of atom coordinates read : 5365 total number of charged atoms : 5195 net assigned charge : -1.499968 assigned positive charge : 818.9024 centred at (gu) : 87.21567 91.77013 91.52760 assigned negative charge : -820.4093 centred at (gu) : 87.27553 91.56754 91.74374 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 94496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42089 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 26597 mr = 67295 m= 2233 mr = 18234 m= 48 mr = 1027 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 5798 time to turn everything in is 0.4600000 number of dielectric boundary points 36816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 38797 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) : 0.5009288 object centre at (A) : 103.0030 25.45850 30.17300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3198236E-04 -5.3016981E-03 midg,1,midg; midg,igrid,midg -7.5283726E-03 8.6723175E-03 1,midg,midg; igrid,midg,midg -1.8429475E-02 7.6498631E-03 gauss-seidel spectral radius is 0.9980676 estimated iterations to convergence 181 setup time was (sec) 0.7000000 now iterating at: 15:23:41 rms-change max change #iterations 3.934683 154.4001 at 10iterations 1.592263 53.12813 at 20iterations 0.6472910 19.54539 at 30iterations 0.2618773 8.727624 at 40iterations 0.1069418 3.381622 at 50iterations 4.3556143E-02 1.326438 at 60iterations 1.7755261E-02 0.5590334 at 70iterations 7.2229956E-03 0.2291603 at 80iterations 2.9644091E-03 9.9099159E-02 at 90iterations 1.2091870E-03 3.7310839E-02 at 100iterations 4.9800094E-04 1.5277863E-02 at 110iterations 2.0765302E-04 6.8588257E-03 at 120iterations finished qdiffx linear iterations at : 15:23:48 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.0765302E-04 6.8588257E-03 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 15:23:48 7.967u 0.176s 0:08.46 96.0% 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 Sun Oct 9 2011 at 15:23:48 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5365 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: 2.254179 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): 67.46900 138.5370 ymin,ymax (A): -6.225000 57.14200 zmin,zma (A): -3.372000 63.71800 x,y,z range (A): 71.06799 63.36700 67.09000 scale (grids/A): 2.254179 object centre (A): 103.0030 25.45850 30.17300 number of atom coordinates read : 5365 total number of charged atoms : 5195 net assigned charge : -1.499968 assigned positive charge : 818.9024 centred at (gu) : 85.82291 92.65482 92.29094 assigned negative charge : -820.4093 centred at (gu) : 85.91332 92.35149 92.61527 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 220967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42089 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 96964 mr = 165012 m= 23917 mr = 77335 m= 3176 mr = 17630 m= 133 mr = 2011 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 19241 time to turn everything in is 1.080000 number of dielectric boundary points 83122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 41449 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) : 1.502786 object centre at (A) : 103.0030 25.45850 30.17300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8137948E-03 -0.1121720 midg,1,midg; midg,igrid,midg -0.1678112 0.2128014 1,midg,midg; igrid,midg,midg -0.5402976 0.3406067 gauss-seidel spectral radius is 0.9991526 estimated iterations to convergence 271 setup time was (sec) 1.330000 now iterating at: 15:23:50 rms-change max change #iterations 10.54631 299.3703 at 10iterations 5.937769 120.2188 at 20iterations 3.329863 85.75594 at 30iterations 1.855714 38.68262 at 40iterations 1.032835 20.95163 at 50iterations 0.5750183 10.53871 at 60iterations 0.3185217 6.031944 at 70iterations 0.1767791 3.001877 at 80iterations 9.8002732E-02 1.993371 at 90iterations 5.4350618E-02 0.9607010 at 100iterations 2.9993257E-02 0.5600824 at 110iterations 1.6612649E-02 0.2816048 at 120iterations 9.1966614E-03 0.1733017 at 130iterations 5.0753406E-03 8.6078644E-02 at 140iterations 2.8155979E-03 5.1548205E-02 at 150iterations 1.5576297E-03 2.5440216E-02 at 160iterations 8.6260133E-04 1.5914917E-02 at 170iterations 4.7703582E-04 9.2735291E-03 at 180iterations finished qdiffx linear iterations at : 15:24:01 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 4.7703582E-04 9.2735291E-03 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 15:24:02 12.969u 0.219s 0:13.53 97.3% 0+0k 0+0io 0pf+0w