Wed Nov 16 17:49:23 PST 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 Wed Nov 16 2011 at 17:49:23 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7481349 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 0.7481349 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 89.07200 90.41683 90.25998 assigned negative charge : -322.8520 centred at (gu) : 89.10596 90.49541 90.43835 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8208 nv = 96 ne = 84 npr = 43483 no. pairs analyzed = 43483 no. exposed pairs = 2728 no. arc points = 19022 no. surface atoms = 924 nbur = 1191 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 587 mr = 4556 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2100000 number of dielectric boundary points 4128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1483 ## 105 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2189999E-08 -3.6090057E-07 midg,1,midg; midg,igrid,midg -2.9017997E-08 -2.3800179E-07 1,midg,midg; igrid,midg,midg -9.8706707E-08 -1.4046230E-07 gauss-seidel spectral radius is 0.9906906 estimated iterations to convergence 84 setup time was (sec) 0.4100000 now iterating at: 17:49:23 rms-change max change #iterations 0.2583637 38.58784 at 10iterations 3.5496376E-02 4.441126 at 20iterations 4.8807766E-03 0.6426315 at 30iterations 6.6545099E-04 7.8256607E-02 at 40iterations 9.3171868E-05 1.1211395E-02 at 50iterations finished qdiffx linear iterations at : 17:49:26 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 9.3171868E-05 1.1211395E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 17:49:27 3.500u 0.186s 0:04.10 89.7% 0+0k 1000+45624io 3pf+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 Wed Nov 16 2011 at 17:49:27 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.244405 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 2.244405 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 87.21589 91.25055 90.78004 assigned negative charge : -322.8520 centred at (gu) : 87.31781 91.48618 91.31506 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 86139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19022 grid for indexing accessible points = 1.400000 m= 34757 mr = 59499 m= 7583 mr = 26304 m= 828 mr = 5164 m= 33 mr = 458 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 284 time to turn everything in is 0.5400000 number of dielectric boundary points 37915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 15766 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) : 0.7481349 object centre at (A) : 1.659500 14.13850 20.29550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4336422E-03 -0.1411038 midg,1,midg; midg,igrid,midg -2.6169872E-02 -3.1417761E-02 1,midg,midg; igrid,midg,midg -1.4544513E-02 -1.0696483E-02 gauss-seidel spectral radius is 0.9989469 estimated iterations to convergence 244 setup time was (sec) 0.7500000 now iterating at: 17:49:28 rms-change max change #iterations 5.212487 218.6230 at 10iterations 2.663622 80.82315 at 20iterations 1.363421 37.74221 at 30iterations 0.6998957 19.44129 at 40iterations 0.3589729 9.805058 at 50iterations 0.1844423 5.075119 at 60iterations 9.4628833E-02 2.808907 at 70iterations 4.8331201E-02 1.349974 at 80iterations 2.4831850E-02 0.6810598 at 90iterations 1.2793644E-02 0.3764343 at 100iterations 6.5375078E-03 0.1888514 at 110iterations 3.3586395E-03 9.7297668E-02 at 120iterations finished qdiffx linear iterations at : 17:49:35 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 3.3586395E-03 9.7297668E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 17:49:36 8.161u 0.225s 0:08.72 96.1% 0+0k 0+45168io 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 Wed Nov 16 2011 at 17:49:36 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.366607 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): -20.87800 24.19700 ymin,ymax (A): -7.979000 36.25600 zmin,zma (A): -3.497000 44.08800 x,y,z range (A): 45.07500 44.23500 47.58500 scale (grids/A): 3.366607 object centre (A): 1.659500 14.13850 20.29550 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 85.82385 91.87578 91.17007 assigned negative charge : -322.8520 centred at (gu) : 85.97677 92.22931 91.97270 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 198376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19022 grid for indexing accessible points = 1.400000 m= 106258 mr = 143451 m= 45636 mr = 87892 m= 14591 mr = 37679 m= 3423 mr = 11435 m= 456 mr = 2534 m= 23 mr = 270 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 917 time to turn everything in is 1.710000 number of dielectric boundary points 85498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 15808 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) : 2.244405 object centre at (A) : 1.659500 14.13850 20.29550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3053623E-02 -1.239041 midg,1,midg; midg,igrid,midg -0.2429096 -0.1675914 1,midg,midg; igrid,midg,midg -0.1827740 -0.1603578 gauss-seidel spectral radius is 0.9993262 estimated iterations to convergence 304 setup time was (sec) 1.950000 now iterating at: 17:49:38 rms-change max change #iterations 11.21751 306.3041 at 10iterations 6.639752 144.5726 at 20iterations 3.941874 92.21180 at 30iterations 2.329015 42.66245 at 40iterations 1.374416 23.49804 at 50iterations 0.8119814 13.44343 at 60iterations 0.4790279 7.419797 at 70iterations 0.2816936 4.490234 at 80iterations 0.1662909 2.670427 at 90iterations 9.8097794E-02 1.561804 at 100iterations 5.7743717E-02 0.8989563 at 110iterations 3.3943821E-02 0.5894241 at 120iterations 2.0018384E-02 0.3354225 at 130iterations 1.1781196E-02 0.1813068 at 140iterations 6.9570625E-03 0.1236119 at 150iterations 4.0950920E-03 7.0023537E-02 at 160iterations 2.4160759E-03 3.6937714E-02 at 170iterations 1.4192318E-03 2.1188736E-02 at 180iterations finished qdiffx linear iterations at : 17:49:49 total time elapsed so far: 13.53000 # loops : 180 mean,max change (kT/e) : 1.4192318E-03 2.1188736E-02 energy calculations done at 13.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.67000 DelPhi exited at 17:49:50 13.679u 0.226s 0:14.19 97.8% 0+0k 0+45160io 0pf+0w