Mon Oct 10 14:04:37 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 Mon Oct 10 2011 at 14:04:37 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 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: 0.5420632 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): -4.054000 42.44000 ymin,ymax (A): 37.50400 88.98600 zmin,zma (A): -3.351000 62.32400 x,y,z range (A): 46.49400 51.48200 65.67500 scale (grids/A): 0.5420632 object centre (A): 19.19300 63.24500 29.48650 number of atom coordinates read : 2567 total number of charged atoms : 2422 net assigned charge : -9.499981 assigned positive charge : 385.3238 centred at (gu) : 90.48864 88.38173 89.92188 assigned negative charge : -394.8243 centred at (gu) : 90.65155 88.08925 89.86728 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4922 nv = 96 ne = 84 npr = 51536 no. pairs analyzed = 51536 no. exposed pairs = 3512 no. arc points = 24944 no. surface atoms = 1173 nbur = 1394 mkacc time = 0.1100000 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 = 1.568000 m= 191 mr = 2343 m= 1 mr = 9 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 0.3000000 number of dielectric boundary points 2762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2505 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6437 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6348577E-10 -1.9214869E-10 midg,1,midg; midg,igrid,midg -3.0276532E-09 6.3285638E-10 1,midg,midg; igrid,midg,midg 2.9672989E-10 -1.4838576E-09 gauss-seidel spectral radius is 0.9824305 estimated iterations to convergence 62 setup time was (sec) 0.5300000 now iterating at: 14:04:38 rms-change max change #iterations 6.6141568E-02 12.66059 at 10iterations 4.2122831E-03 0.7453518 at 20iterations 2.7458841E-04 5.1868081E-02 at 30iterations 1.8812234E-05 3.3721924E-03 at 40iterations 1.4650227E-06 2.3794174E-04 at 50iterations finished qdiffx linear iterations at : 14:04:41 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 1.4650227E-06 2.3794174E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 14:04:42 3.289u 0.218s 0:04.12 84.7% 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 Mon Oct 10 2011 at 14:04:42 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 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: 1.626190 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): -4.054000 42.44000 ymin,ymax (A): 37.50400 88.98600 zmin,zma (A): -3.351000 62.32400 x,y,z range (A): 46.49400 51.48200 65.67500 scale (grids/A): 1.626190 object centre (A): 19.19300 63.24500 29.48650 number of atom coordinates read : 2567 total number of charged atoms : 2422 net assigned charge : -9.499981 assigned positive charge : 385.3238 centred at (gu) : 91.46552 85.14476 89.76511 assigned negative charge : -394.8243 centred at (gu) : 91.95442 84.26741 89.60155 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 53853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24944 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16042 mr = 34373 m= 1478 mr = 10659 m= 38 mr = 657 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 217 time to turn everything in is 0.4100000 number of dielectric boundary points 25722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 18460 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) : 0.5420632 object centre at (A) : 19.19300 63.24500 29.48650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8230835E-02 4.1664643E-03 midg,1,midg; midg,igrid,midg -2.4348706E-02 2.9568661E-03 1,midg,midg; igrid,midg,midg -2.2112296E-03 -1.0045047E-02 gauss-seidel spectral radius is 0.9981203 estimated iterations to convergence 183 setup time was (sec) 0.7000000 now iterating at: 14:04:43 rms-change max change #iterations 3.057107 138.7870 at 10iterations 1.258081 51.10861 at 20iterations 0.5133388 20.78037 at 30iterations 0.2103251 8.344849 at 40iterations 8.6394615E-02 3.537575 at 50iterations 3.5369292E-02 1.344460 at 60iterations 1.4503532E-02 0.6837645 at 70iterations 5.9423833E-03 0.2287292 at 80iterations 2.4314772E-03 9.9773407E-02 at 90iterations 9.9924125E-04 3.6714792E-02 at 100iterations 4.0868128E-04 1.4897823E-02 at 110iterations 1.6830083E-04 7.1296692E-03 at 120iterations finished qdiffx linear iterations at : 14:04:49 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 1.6830083E-04 7.1296692E-03 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 14:04:50 7.330u 0.246s 0:07.89 95.9% 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 Mon Oct 10 2011 at 14:04:50 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 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: 2.439285 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): -4.054000 42.44000 ymin,ymax (A): 37.50400 88.98600 zmin,zma (A): -3.351000 62.32400 x,y,z range (A): 46.49400 51.48200 65.67500 scale (grids/A): 2.439285 object centre (A): 19.19300 63.24500 29.48650 number of atom coordinates read : 2567 total number of charged atoms : 2422 net assigned charge : -9.499981 assigned positive charge : 385.3238 centred at (gu) : 92.19816 82.71693 89.64764 assigned negative charge : -394.8243 centred at (gu) : 92.93157 81.40106 89.40224 start vw surface at 0.1400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 124705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24944 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 56154 mr = 84328 m= 15075 mr = 43505 m= 2142 mr = 11002 m= 120 mr = 1295 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 719 time to turn everything in is 0.9400000 number of dielectric boundary points 58029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19357 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) : 1.626190 object centre at (A) : 19.19300 63.24500 29.48650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7692745 3.8125210E-02 midg,1,midg; midg,igrid,midg -0.3421115 6.2883884E-02 1,midg,midg; igrid,midg,midg -3.8856328E-02 -0.1319197 gauss-seidel spectral radius is 0.9991079 estimated iterations to convergence 265 setup time was (sec) 1.250000 now iterating at: 14:04:51 rms-change max change #iterations 8.002034 277.2693 at 10iterations 4.442840 125.2469 at 20iterations 2.459707 68.46066 at 30iterations 1.356057 37.05764 at 40iterations 0.7466941 18.00168 at 50iterations 0.4104155 9.246341 at 60iterations 0.2242160 5.295696 at 70iterations 0.1227599 2.772316 at 80iterations 6.7097589E-02 1.706342 at 90iterations 3.6546666E-02 0.8146076 at 100iterations 1.9878302E-02 0.4375825 at 110iterations 1.0870839E-02 0.2355042 at 120iterations 5.9168818E-03 0.1336060 at 130iterations 3.2195498E-03 7.2745502E-02 at 140iterations 1.7458927E-03 4.1814446E-02 at 150iterations 9.5112383E-04 2.1029472E-02 at 160iterations 5.1723787E-04 1.2361526E-02 at 170iterations 2.8092158E-04 6.8025589E-03 at 180iterations finished qdiffx linear iterations at : 14:05:01 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 2.8092158E-04 6.8025589E-03 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 14:05:02 11.565u 0.248s 0:12.20 96.7% 0+0k 0+0io 0pf+0w