Sat Oct 15 14:21:32 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 14:21:32 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3274 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: 0.6607153 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): 12.92300 62.60300 ymin,ymax (A): -40.95300 10.18700 zmin,zma (A): 31.46900 85.35000 x,y,z range (A): 49.68000 51.14000 53.88100 scale (grids/A): 0.6607153 object centre (A): 37.76300 -15.38300 58.40950 number of atom coordinates read : 3274 total number of charged atoms : 3126 net assigned charge : 2.000037 assigned positive charge : 497.0557 centred at (gu) : 89.22189 91.32753 89.65554 assigned negative charge : -495.0566 centred at (gu) : 89.30007 91.30793 89.69493 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 9339 nv = 96 ne = 84 npr = 68853 no. pairs analyzed = 68853 no. exposed pairs = 3532 no. arc points = 24453 no. surface atoms = 1213 nbur = 2061 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 586 mr = 5618 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2371 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 11300 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6068162E-08 -4.8663016E-09 midg,1,midg; midg,igrid,midg -4.9532305E-11 1.3054907E-08 1,midg,midg; igrid,midg,midg 2.9195240E-08 -1.2965990E-08 gauss-seidel spectral radius is 0.9881749 estimated iterations to convergence 75 setup time was (sec) 0.4500000 now iterating at: 14:21:33 rms-change max change #iterations 0.1962719 26.07288 at 10iterations 2.1034440E-02 2.760910 at 20iterations 2.4308516E-03 0.3077545 at 30iterations 4.3750592E-04 6.3350677E-02 at 40iterations 1.5804151E-04 2.4585724E-02 at 50iterations finished qdiffx linear iterations at : 14:21:36 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 1.5804151E-04 2.4585724E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 14:21:37 3.658u 0.205s 0:04.15 92.7% 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 Sat Oct 15 2011 at 14:21:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3274 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: 1.982146 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): 12.92300 62.60300 ymin,ymax (A): -40.95300 10.18700 zmin,zma (A): 31.46900 85.35000 x,y,z range (A): 49.68000 51.14000 53.88100 scale (grids/A): 1.982146 object centre (A): 37.76300 -15.38300 58.40950 number of atom coordinates read : 3274 total number of charged atoms : 3126 net assigned charge : 2.000037 assigned positive charge : 497.0557 centred at (gu) : 87.66474 93.98174 88.96558 assigned negative charge : -495.0566 centred at (gu) : 87.89982 93.92326 89.08443 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 100888 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24453 grid for indexing accessible points = 1.400000 m= 40102 mr = 73920 m= 7438 mr = 31084 m= 607 mr = 5004 m= 10 mr = 272 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.5200000 number of dielectric boundary points 38765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 24688 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) : 0.6607153 object centre at (A) : 37.76300 -15.38300 58.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0377944E-02 -1.8761361E-02 midg,1,midg; midg,igrid,midg 1.2035216E-03 2.8896911E-02 1,midg,midg; igrid,midg,midg 3.0137502E-02 4.1497283E-02 gauss-seidel spectral radius is 0.9987801 estimated iterations to convergence 227 setup time was (sec) 0.7600000 now iterating at: 14:21:38 rms-change max change #iterations 5.253568 187.0035 at 10iterations 2.565207 72.26080 at 20iterations 1.259082 34.22153 at 30iterations 0.6163464 16.31920 at 40iterations 0.3027951 8.942095 at 50iterations 0.1477774 3.804881 at 60iterations 7.2488129E-02 2.050896 at 70iterations 3.5487197E-02 1.101042 at 80iterations 1.7450999E-02 0.4541340 at 90iterations 8.5683232E-03 0.2412968 at 100iterations 4.2476207E-03 0.1145401 at 110iterations 2.1335427E-03 5.7197571E-02 at 120iterations finished qdiffx linear iterations at : 14:21:45 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 2.1335427E-03 5.7197571E-02 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 14:21:46 8.602u 0.228s 0:09.18 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 Sat Oct 15 2011 at 14:21:46 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3274 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: 2.973219 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): 12.92300 62.60300 ymin,ymax (A): -40.95300 10.18700 zmin,zma (A): 31.46900 85.35000 x,y,z range (A): 49.68000 51.14000 53.88100 scale (grids/A): 2.973219 object centre (A): 37.76300 -15.38300 58.40950 number of atom coordinates read : 3274 total number of charged atoms : 3126 net assigned charge : 2.000037 assigned positive charge : 497.0557 centred at (gu) : 86.49696 95.97231 88.44829 assigned negative charge : -495.0566 centred at (gu) : 86.84936 95.88486 88.62653 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 233068 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24453 grid for indexing accessible points = 1.400000 m= 126803 mr = 177705 m= 50134 mr = 107206 m= 13878 mr = 41781 m= 2573 mr = 10774 m= 282 mr = 1815 m= 8 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 1154 time to turn everything in is 1.320000 number of dielectric boundary points 87328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 25008 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) : 1.982146 object centre at (A) : 37.76300 -15.38300 58.40950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1033869 -7.2377592E-02 midg,1,midg; midg,igrid,midg -4.9413119E-02 0.3152262 1,midg,midg; igrid,midg,midg 0.2477583 0.5413219 gauss-seidel spectral radius is 0.9993005 estimated iterations to convergence 298 setup time was (sec) 1.590000 now iterating at: 14:21:48 rms-change max change #iterations 11.99935 433.2914 at 10iterations 7.155247 190.9804 at 20iterations 4.247463 75.90797 at 30iterations 2.517389 41.01678 at 40iterations 1.485849 27.88379 at 50iterations 0.8767078 15.16824 at 60iterations 0.5157227 8.362476 at 70iterations 0.3028086 4.660853 at 80iterations 0.1775172 2.800953 at 90iterations 0.1041743 1.563218 at 100iterations 6.1053738E-02 1.046186 at 110iterations 3.5840426E-02 0.5403538 at 120iterations 2.0982405E-02 0.3364458 at 130iterations 1.2293857E-02 0.1947846 at 140iterations 7.2177104E-03 0.1077071 at 150iterations 4.2433999E-03 6.5029144E-02 at 160iterations 2.4977159E-03 4.1027069E-02 at 170iterations 1.4849211E-03 2.3986816E-02 at 180iterations finished qdiffx linear iterations at : 14:22:12 total time elapsed so far: 14.01000 # loops : 180 mean,max change (kT/e) : 1.4849211E-03 2.3986816E-02 energy calculations done at 14.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.14000 DelPhi exited at 14:22:13 14.142u 0.267s 0:27.18 52.9% 0+0k 0+0io 0pf+0w