Sat Oct 15 13:53:43 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 13:53:43 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: GLM 105 has a net charge of -0.0940 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: 0.5683995 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): -14.52400 39.93600 ymin,ymax (A): -22.08900 23.09300 zmin,zma (A): -17.07900 45.55300 x,y,z range (A): 54.46000 45.18200 62.63200 scale (grids/A): 0.5683995 object centre (A): 12.70600 0.5019999 14.23700 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : 0.4060311 assigned positive charge : 445.8442 centred at (gu) : 90.02818 89.29932 89.97640 assigned negative charge : -445.4393 centred at (gu) : 90.00746 89.41589 90.03440 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6342 nv = 96 ne = 84 npr = 59409 no. pairs analyzed = 59409 no. exposed pairs = 3764 no. arc points = 27155 no. surface atoms = 1274 nbur = 1698 mkacc time = 9.9999994E-02 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 = 1.512000 m= 273 mr = 3302 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2200000 number of dielectric boundary points 3294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2713 ## 283 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8069 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0988195E-10 -8.2001167E-10 midg,1,midg; midg,igrid,midg 2.0866586E-09 -1.4484293E-09 1,midg,midg; igrid,midg,midg -2.6171651E-10 3.5653619E-10 gauss-seidel spectral radius is 0.9840334 estimated iterations to convergence 65 setup time was (sec) 0.4500000 now iterating at: 13:53:43 rms-change max change #iterations 9.1742814E-02 14.39571 at 10iterations 6.7606042E-03 1.101908 at 20iterations 5.0233077E-04 8.2328796E-02 at 30iterations 4.1657942E-05 7.4720383E-03 at 40iterations 5.3394974E-06 1.1634827E-03 at 50iterations finished qdiffx linear iterations at : 13:53:46 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 5.3394974E-06 1.1634827E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 13:53:47 3.740u 0.219s 0:04.28 92.2% 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 13:53:47 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: GLM 105 has a net charge of -0.0940 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: 1.705199 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): -14.52400 39.93600 ymin,ymax (A): -22.08900 23.09300 zmin,zma (A): -17.07900 45.55300 x,y,z range (A): 54.46000 45.18200 62.63200 scale (grids/A): 1.705199 object centre (A): 12.70600 0.5019999 14.23700 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : 0.4060311 assigned positive charge : 445.8442 centred at (gu) : 90.08421 87.89743 89.92840 assigned negative charge : -445.4393 centred at (gu) : 90.02203 88.24727 90.10318 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27155 grid for indexing accessible points = 1.400000 m= 22373 mr = 46537 m= 2674 mr = 15729 m= 78 mr = 1347 m= 0 mr = 18 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 955 time to turn everything in is 0.3500000 number of dielectric boundary points 30680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 283 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21854 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) : 0.5683995 object centre at (A) : 12.70600 0.5019999 14.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8995864E-03 -1.6505649E-02 midg,1,midg; midg,igrid,midg 1.2467750E-02 -6.6773803E-03 1,midg,midg; igrid,midg,midg 3.9789211E-03 9.2865888E-04 gauss-seidel spectral radius is 0.9983463 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 13:53:48 rms-change max change #iterations 3.689444 171.1299 at 10iterations 1.590358 61.60463 at 20iterations 0.6888650 23.75317 at 30iterations 0.2988925 10.47151 at 40iterations 0.1298460 4.480620 at 50iterations 5.6386974E-02 2.011194 at 60iterations 2.4442358E-02 0.8671573 at 70iterations 1.0589234E-02 0.3864822 at 80iterations 4.6093278E-03 0.1547365 at 90iterations 2.0193888E-03 6.6591740E-02 at 100iterations 8.7657489E-04 3.0441284E-02 at 110iterations 3.8647154E-04 1.2747288E-02 at 120iterations finished qdiffx linear iterations at : 13:54:01 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 3.8647154E-04 1.2747288E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 13:54:02 7.983u 0.241s 0:14.62 56.2% 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 13:54:02 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: GLM 105 has a net charge of -0.0940 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: 2.557798 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): -14.52400 39.93600 ymin,ymax (A): -22.08900 23.09300 zmin,zma (A): -17.07900 45.55300 x,y,z range (A): 54.46000 45.18200 62.63200 scale (grids/A): 2.557798 object centre (A): 12.70600 0.5019999 14.23700 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : 0.4060311 assigned positive charge : 445.8442 centred at (gu) : 90.12601 86.84599 89.89247 assigned negative charge : -445.4393 centred at (gu) : 90.03289 87.37075 90.15458 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 160371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27155 grid for indexing accessible points = 1.400000 m= 75547 mr = 113835 m= 23858 mr = 59992 m= 4217 mr = 18290 m= 372 mr = 2870 m= 5 mr = 193 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 3323 time to turn everything in is 0.8900000 number of dielectric boundary points 69190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 22592 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) : 1.705199 object centre at (A) : 12.70600 0.5019999 14.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1984921 -0.2278854 midg,1,midg; midg,igrid,midg 0.1367133 -8.0540173E-02 1,midg,midg; igrid,midg,midg 3.4873929E-02 0.1174526 gauss-seidel spectral radius is 0.9991895 estimated iterations to convergence 277 setup time was (sec) 1.180000 now iterating at: 13:54:03 rms-change max change #iterations 9.238239 311.7963 at 10iterations 5.230505 120.3027 at 20iterations 2.944493 72.04831 at 30iterations 1.660539 33.83628 at 40iterations 0.9343101 19.44848 at 50iterations 0.5234420 10.70651 at 60iterations 0.2931620 6.015522 at 70iterations 0.1640230 3.544680 at 80iterations 9.2114404E-02 1.821895 at 90iterations 5.1553104E-02 0.9845152 at 100iterations 2.8848968E-02 0.5774050 at 110iterations 1.6103152E-02 0.3196726 at 120iterations 9.0211760E-03 0.1844902 at 130iterations 5.0611002E-03 0.1096148 at 140iterations 2.8387669E-03 6.0714722E-02 at 150iterations 1.5913817E-03 3.0689240E-02 at 160iterations 8.9439505E-04 1.6952276E-02 at 170iterations 5.0688774E-04 1.0340839E-02 at 180iterations finished qdiffx linear iterations at : 13:54:16 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 5.0688774E-04 1.0340839E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.90000 DelPhi exited at 13:54:17 13.905u 0.283s 0:15.02 94.4% 0+0k 0+0io 0pf+0w