Mon Oct 10 23:39:47 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 23:39:47 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 262 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5697733 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): 11.33400 64.66300 ymin,ymax (A): -3.434000 59.04700 zmin,zma (A): 10.96400 54.18900 x,y,z range (A): 53.32900 62.48100 43.22500 scale (grids/A): 0.5697733 object centre (A): 37.99850 27.80650 32.57650 number of atom coordinates read : 2656 total number of charged atoms : 2511 net assigned charge : 7.906016 assigned positive charge : 402.8888 centred at (gu) : 88.82671 91.28472 89.85286 assigned negative charge : -394.9833 centred at (gu) : 88.79933 91.11103 89.98503 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5639 nv = 96 ne = 84 npr = 52911 no. pairs analyzed = 52911 no. exposed pairs = 3186 no. arc points = 22594 no. surface atoms = 1081 nbur = 1575 mkacc time = 0.1300000 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= 253 mr = 3087 m= 0 mr = 16 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3600000 number of dielectric boundary points 2789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2232 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0728819E-09 -6.5963696E-10 midg,1,midg; midg,igrid,midg -9.2676283E-10 4.7914934E-09 1,midg,midg; igrid,midg,midg 1.0303380E-09 1.1790660E-09 gauss-seidel spectral radius is 0.9840769 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 23:39:48 rms-change max change #iterations 8.9876257E-02 14.13872 at 10iterations 7.9711219E-03 1.418182 at 20iterations 1.1321410E-03 0.2584991 at 30iterations 2.7993848E-04 6.9469452E-02 at 40iterations 7.4468779E-05 1.8730164E-02 at 50iterations finished qdiffx linear iterations at : 23:39:51 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 7.4468779E-05 1.8730164E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 23:39:51 3.418u 0.139s 0:03.88 91.2% 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 Mon Oct 10 2011 at 23:39:51 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 262 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.709320 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): 11.33400 64.66300 ymin,ymax (A): -3.434000 59.04700 zmin,zma (A): 10.96400 54.18900 x,y,z range (A): 53.32900 62.48100 43.22500 scale (grids/A): 1.709320 object centre (A): 37.99850 27.80650 32.57650 number of atom coordinates read : 2656 total number of charged atoms : 2511 net assigned charge : 7.906016 assigned positive charge : 402.8888 centred at (gu) : 86.47961 93.85393 89.55807 assigned negative charge : -394.9833 centred at (gu) : 86.39742 93.33274 89.95475 start vw surface at 0.2400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 61892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22594 grid for indexing accessible points = 1.400000 m= 20343 mr = 42912 m= 2481 mr = 14631 m= 64 mr = 1340 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 764 time to turn everything in is 0.5500000 number of dielectric boundary points 25893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19442 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) : 0.5697733 object centre at (A) : 37.99850 27.80650 32.57650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9340158E-02 3.0055752E-03 midg,1,midg; midg,igrid,midg -5.9457486E-03 -7.6616104E-03 1,midg,midg; igrid,midg,midg -1.8267038E-04 1.0822309E-02 gauss-seidel spectral radius is 0.9983108 estimated iterations to convergence 193 setup time was (sec) 0.8200000 now iterating at: 23:39:52 rms-change max change #iterations 3.437691 168.8281 at 10iterations 1.476049 59.41301 at 20iterations 0.6368021 23.74195 at 30iterations 0.2738824 9.962357 at 40iterations 0.1181505 4.384716 at 50iterations 5.1364228E-02 1.848333 at 60iterations 2.2240080E-02 0.8906937 at 70iterations 9.7454302E-03 0.3588638 at 80iterations 4.3887268E-03 0.1825905 at 90iterations 2.0822734E-03 8.9210510E-02 at 100iterations 1.0503909E-03 4.8700333E-02 at 110iterations 5.6424632E-04 2.5794983E-02 at 120iterations finished qdiffx linear iterations at : 23:39:59 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 5.6424632E-04 2.5794983E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 23:39:59 7.371u 0.192s 0:07.88 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 23:39:59 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 262 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.563980 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): 11.33400 64.66300 ymin,ymax (A): -3.434000 59.04700 zmin,zma (A): 10.96400 54.18900 x,y,z range (A): 53.32900 62.48100 43.22500 scale (grids/A): 2.563980 object centre (A): 37.99850 27.80650 32.57650 number of atom coordinates read : 2656 total number of charged atoms : 2511 net assigned charge : 7.906016 assigned positive charge : 402.8888 centred at (gu) : 84.71938 95.78082 89.33688 assigned negative charge : -394.9833 centred at (gu) : 84.59602 94.99907 89.93192 start vw surface at 0.2100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 143797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22594 grid for indexing accessible points = 1.400000 m= 68849 mr = 104623 m= 21686 mr = 55707 m= 4060 mr = 16902 m= 317 mr = 2841 m= 5 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2562 time to turn everything in is 1.190000 number of dielectric boundary points 58496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 20080 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) : 1.709320 object centre at (A) : 37.99850 27.80650 32.57650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2511132 5.7817992E-02 midg,1,midg; midg,igrid,midg -0.1564584 -0.4837100 1,midg,midg; igrid,midg,midg -4.3775067E-02 0.1106979 gauss-seidel spectral radius is 0.9991630 estimated iterations to convergence 273 setup time was (sec) 1.490000 now iterating at: 23:40:01 rms-change max change #iterations 8.634901 316.7820 at 10iterations 4.836679 123.8981 at 20iterations 2.709597 62.36135 at 30iterations 1.514893 33.02422 at 40iterations 0.8442636 19.09211 at 50iterations 0.4700029 9.662148 at 60iterations 0.2610928 5.216434 at 70iterations 0.1453174 3.043625 at 80iterations 8.0859408E-02 1.616486 at 90iterations 4.4896424E-02 0.9309883 at 100iterations 2.4970870E-02 0.5027237 at 110iterations 1.3917826E-02 0.2770767 at 120iterations 7.8099300E-03 0.1635208 at 130iterations 4.4028722E-03 9.5661163E-02 at 140iterations 2.5223286E-03 5.6646347E-02 at 150iterations 1.4920956E-03 3.6087036E-02 at 160iterations 9.1406942E-04 2.2525787E-02 at 170iterations 5.8596220E-04 1.5335083E-02 at 180iterations finished qdiffx linear iterations at : 23:40:12 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 5.8596220E-04 1.5335083E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 23:40:12 12.766u 0.183s 0:13.26 97.5% 0+0k 0+0io 0pf+0w