Sat Oct 8 17:26:36 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 8 2011 at 17:26:36 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3798 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5537151 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): -1.943000 60.52500 ymin,ymax (A): -18.46000 44.64600 zmin,zma (A): -5.378000 58.91500 x,y,z range (A): 62.46800 63.10600 64.29300 scale (grids/A): 0.5537151 object centre (A): 29.29100 13.09300 26.76850 number of atom coordinates read : 3798 total number of charged atoms : 3647 net assigned charge : -8.499977 assigned positive charge : 578.7823 centred at (gu) : 88.83598 86.69198 90.53808 assigned negative charge : -587.2848 centred at (gu) : 88.91594 86.70708 90.53868 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7618 nv = 96 ne = 84 npr = 76716 no. pairs analyzed = 76716 no. exposed pairs = 4956 no. arc points = 34531 no. surface atoms = 1642 nbur = 2156 mkacc time = 0.1600000 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= 332 mr = 3956 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3447 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2832722E-10 -8.2666374E-10 midg,1,midg; midg,igrid,midg -1.2021950E-09 -4.1141074E-10 1,midg,midg; igrid,midg,midg 2.6612715E-10 -1.2439297E-09 gauss-seidel spectral radius is 0.9832444 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 17:26:37 rms-change max change #iterations 9.1966376E-02 14.68837 at 10iterations 6.4191828E-03 1.091395 at 20iterations 4.8212596E-04 6.7798615E-02 at 30iterations 5.6541194E-05 9.0250969E-03 at 40iterations 1.2366916E-05 2.0875931E-03 at 50iterations finished qdiffx linear iterations at : 17:26:39 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.2366916E-05 2.0875931E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 17:26:40 3.185u 0.140s 0:03.75 88.5% 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 17:26:40 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3798 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.661145 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): -1.943000 60.52500 ymin,ymax (A): -18.46000 44.64600 zmin,zma (A): -5.378000 58.91500 x,y,z range (A): 62.46800 63.10600 64.29300 scale (grids/A): 1.661145 object centre (A): 29.29100 13.09300 26.76850 number of atom coordinates read : 3798 total number of charged atoms : 3647 net assigned charge : -8.499977 assigned positive charge : 578.7823 centred at (gu) : 86.50671 80.07471 91.61285 assigned negative charge : -587.2848 centred at (gu) : 86.74756 80.12080 91.61588 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34531 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26560 mr = 57669 m= 2887 mr = 18060 m= 87 mr = 1292 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 196 time to turn everything in is 0.5800000 number of dielectric boundary points 37019 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 380 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 28012 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) : 0.5537151 object centre at (A) : 29.29100 13.09300 26.76850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2779026E-03 -1.8220963E-03 midg,1,midg; midg,igrid,midg -1.9554922E-02 -8.7240702E-03 1,midg,midg; igrid,midg,midg -1.2232599E-02 -3.6238302E-02 gauss-seidel spectral radius is 0.9983230 estimated iterations to convergence 194 setup time was (sec) 0.8300000 now iterating at: 17:26:41 rms-change max change #iterations 4.064043 180.1935 at 10iterations 1.744041 61.76835 at 20iterations 0.7526756 25.37281 at 30iterations 0.3252282 10.57463 at 40iterations 0.1401864 4.853946 at 50iterations 6.0515612E-02 2.055246 at 60iterations 2.6024451E-02 0.7806597 at 70iterations 1.1240700E-02 0.3667765 at 80iterations 4.8789694E-03 0.1656075 at 90iterations 2.1122550E-03 6.6127777E-02 at 100iterations 9.1507344E-04 2.8285980E-02 at 110iterations 4.0017755E-04 1.2018085E-02 at 120iterations finished qdiffx linear iterations at : 17:26:47 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 4.0017755E-04 1.2018085E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 17:26:47 7.007u 0.169s 0:07.44 96.2% 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 8 2011 at 17:26:47 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3798 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.491718 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): -1.943000 60.52500 ymin,ymax (A): -18.46000 44.64600 zmin,zma (A): -5.378000 58.91500 x,y,z range (A): 62.46800 63.10600 64.29300 scale (grids/A): 2.491718 object centre (A): 29.29100 13.09300 26.76850 number of atom coordinates read : 3798 total number of charged atoms : 3647 net assigned charge : -8.499977 assigned positive charge : 578.7823 centred at (gu) : 84.75982 75.11172 92.41896 assigned negative charge : -587.2848 centred at (gu) : 85.12122 75.18111 92.42369 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 196023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34531 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91901 mr = 140837 m= 26442 mr = 72314 m= 4433 mr = 19564 m= 306 mr = 2738 m= 4 mr = 81 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 705 time to turn everything in is 1.440000 number of dielectric boundary points 83576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 29143 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) : 1.661145 object centre at (A) : 29.29100 13.09300 26.76850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3194319E-03 0.1778120 midg,1,midg; midg,igrid,midg -0.3050449 -0.1061438 1,midg,midg; igrid,midg,midg -0.1813332 -0.6373800 gauss-seidel spectral radius is 0.9991955 estimated iterations to convergence 278 setup time was (sec) 1.760000 now iterating at: 17:26:49 rms-change max change #iterations 10.35120 295.9497 at 10iterations 5.944334 145.3726 at 20iterations 3.401345 77.29057 at 30iterations 1.933600 40.35081 at 40iterations 1.096797 21.72558 at 50iterations 0.6192406 12.61253 at 60iterations 0.3499931 6.529131 at 70iterations 0.1974094 3.488694 at 80iterations 0.1111164 2.231422 at 90iterations 6.2510058E-02 1.265274 at 100iterations 3.5129480E-02 0.6577301 at 110iterations 1.9773999E-02 0.3451109 at 120iterations 1.1104870E-02 0.2107720 at 130iterations 6.2263170E-03 0.1220330 at 140iterations 3.5022788E-03 6.1393738E-02 at 150iterations 1.9724800E-03 3.9691925E-02 at 160iterations 1.1079075E-03 2.1307945E-02 at 170iterations 6.2577066E-04 1.1709690E-02 at 180iterations finished qdiffx linear iterations at : 17:27:02 total time elapsed so far: 14.30000 # loops : 180 mean,max change (kT/e) : 6.2577066E-04 1.1709690E-02 energy calculations done at 14.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.47000 DelPhi exited at 17:27:02 14.476u 0.282s 0:15.10 97.6% 0+0k 0+0io 0pf+0w