Sat Oct 8 11:37:18 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+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 Sat Oct 8 2011 at 11:37:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2669 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5761916 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): -37.49600 19.20800 ymin,ymax (A): -27.30700 34.47800 zmin,zma (A): -7.298000 44.29600 x,y,z range (A): 56.70400 61.78500 51.59400 scale (grids/A): 0.5761916 object centre (A): -9.143999 3.585500 18.49900 number of atom coordinates read : 2669 total number of charged atoms : 2519 net assigned charge : 0.5000081 assigned positive charge : 388.0687 centred at (gu) : 91.02365 89.55968 88.93509 assigned negative charge : -387.5694 centred at (gu) : 91.05686 89.48121 88.95766 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5898 nv = 96 ne = 84 npr = 52475 no. pairs analyzed = 52475 no. exposed pairs = 3583 no. arc points = 25747 no. surface atoms = 1215 nbur = 1454 mkacc time = 0.1400000 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 = 1.484000 m= 216 mr = 2848 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2555 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7405 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2450484E-10 -2.1422365E-10 midg,1,midg; midg,igrid,midg -1.3698001E-09 1.2745044E-09 1,midg,midg; igrid,midg,midg 5.1979809E-10 -5.8776478E-10 gauss-seidel spectral radius is 0.9844402 estimated iterations to convergence 66 setup time was (sec) 0.8300000 now iterating at: 11:37:19 rms-change max change #iterations 8.7823272E-02 15.00531 at 10iterations 6.5263854E-03 1.076100 at 20iterations 4.9980066E-04 7.8907967E-02 at 30iterations 3.8928534E-05 5.9673786E-03 at 40iterations 3.2451194E-06 5.7983398E-04 at 50iterations finished qdiffx linear iterations at : 11:37:25 total time elapsed so far: 6.920000 # loops : 50 mean,max change (kT/e) : 3.2451194E-06 5.7983398E-04 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 11:37:26 7.114u 0.709s 0:08.07 96.7% 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 8 2011 at 11:37:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2669 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.728575 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): -37.49600 19.20800 ymin,ymax (A): -27.30700 34.47800 zmin,zma (A): -7.298000 44.29600 x,y,z range (A): 56.70400 61.78500 51.59400 scale (grids/A): 1.728575 object centre (A): -9.143999 3.585500 18.49900 number of atom coordinates read : 2669 total number of charged atoms : 2519 net assigned charge : 0.5000081 assigned positive charge : 388.0687 centred at (gu) : 93.07048 88.67814 86.80470 assigned negative charge : -387.5694 centred at (gu) : 93.17019 88.44325 86.87267 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25747 grid for indexing accessible points = 1.400000 m= 19351 mr = 41618 m= 2138 mr = 13185 m= 72 mr = 983 m= 0 mr = 9 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 174 time to turn everything in is 0.6600000 number of dielectric boundary points 30158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 19516 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) : 0.5761916 object centre at (A) : -9.143999 3.585500 18.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6709701E-03 -1.0095141E-02 midg,1,midg; midg,igrid,midg -1.3571871E-02 -1.0391729E-03 1,midg,midg; igrid,midg,midg 1.2449815E-03 1.2100468E-02 gauss-seidel spectral radius is 0.9983701 estimated iterations to convergence 197 setup time was (sec) 1.200000 now iterating at: 11:37:28 rms-change max change #iterations 3.454938 177.5261 at 10iterations 1.500095 52.75989 at 20iterations 0.6517605 24.20683 at 30iterations 0.2833224 10.31055 at 40iterations 0.1240028 4.413854 at 50iterations 5.3851455E-02 2.063564 at 60iterations 2.3493430E-02 0.8506088 at 70iterations 1.0243508E-02 0.3880997 at 80iterations 4.4643464E-03 0.1740990 at 90iterations 1.9516551E-03 6.8725586E-02 at 100iterations 8.5144828E-04 3.1436920E-02 at 110iterations 3.7291282E-04 1.4835358E-02 at 120iterations finished qdiffx linear iterations at : 11:37:44 total time elapsed so far: 17.14000 # loops : 120 mean,max change (kT/e) : 3.7291282E-04 1.4835358E-02 energy calculations done at 17.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.31000 DelPhi exited at 11:37:45 17.319u 0.883s 0:18.74 97.0% 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 8 2011 at 11:37:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2669 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.592862 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): -37.49600 19.20800 ymin,ymax (A): -27.30700 34.47800 zmin,zma (A): -7.298000 44.29600 x,y,z range (A): 56.70400 61.78500 51.59400 scale (grids/A): 2.592862 object centre (A): -9.143999 3.585500 18.49900 number of atom coordinates read : 2669 total number of charged atoms : 2519 net assigned charge : 0.5000081 assigned positive charge : 388.0687 centred at (gu) : 94.60570 88.01721 85.20686 assigned negative charge : -387.5694 centred at (gu) : 94.75539 87.66489 85.30902 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 149066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25747 grid for indexing accessible points = 1.400000 m= 66049 mr = 102039 m= 19704 mr = 51364 m= 3274 mr = 14712 m= 274 mr = 2042 m= 5 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 569 time to turn everything in is 1.610000 number of dielectric boundary points 68088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 20140 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) : 1.728575 object centre at (A) : -9.143999 3.585500 18.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4361414E-02 -0.1562159 midg,1,midg; midg,igrid,midg -0.1907385 5.5780586E-02 1,midg,midg; igrid,midg,midg -1.7077833E-02 0.2132566 gauss-seidel spectral radius is 0.9991933 estimated iterations to convergence 278 setup time was (sec) 2.230000 now iterating at: 11:37:48 rms-change max change #iterations 8.745278 381.7243 at 10iterations 5.027488 152.5771 at 20iterations 2.882039 62.07070 at 30iterations 1.634520 42.11405 at 40iterations 0.9264327 21.14072 at 50iterations 0.5222671 11.40816 at 60iterations 0.2946964 6.482895 at 70iterations 0.1655481 3.354757 at 80iterations 9.3456663E-02 1.998184 at 90iterations 5.2355334E-02 1.079475 at 100iterations 2.9448586E-02 0.6234088 at 110iterations 1.6492400E-02 0.3832325 at 120iterations 9.2835100E-03 0.1997910 at 130iterations 5.2022692E-03 0.1020241 at 140iterations 2.9159565E-03 6.3482285E-02 at 150iterations 1.6381072E-03 3.1243801E-02 at 160iterations 9.1790291E-04 2.3479462E-02 at 170iterations 5.1597331E-04 1.0368347E-02 at 180iterations finished qdiffx linear iterations at : 11:38:17 total time elapsed so far: 30.75000 # loops : 180 mean,max change (kT/e) : 5.1597331E-04 1.0368347E-02 energy calculations done at 30.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.96000 DelPhi exited at 11:38:17 30.967u 0.845s 0:32.36 98.2% 0+0k 0+0io 0pf+0w