Sun Oct 9 00:05:23 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 Sun Oct 9 2011 at 00:05:23 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2248 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6395745 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): 0.4799999 53.56700 ymin,ymax (A): 8.077000 51.51500 zmin,zma (A): -7.521000 48.14100 x,y,z range (A): 53.08700 43.43800 55.66200 scale (grids/A): 0.6395745 object centre (A): 27.02350 29.79600 20.31000 number of atom coordinates read : 2248 total number of charged atoms : 2114 net assigned charge : 10.51402 assigned positive charge : 327.8566 centred at (gu) : 89.07653 90.89790 89.37801 assigned negative charge : -317.3432 centred at (gu) : 89.04276 90.81540 89.38118 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6354 nv = 96 ne = 84 npr = 44751 no. pairs analyzed = 44751 no. exposed pairs = 3105 no. arc points = 22020 no. surface atoms = 1030 nbur = 1218 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3215 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2145 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7440 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7462144E-08 1.2978984E-08 midg,1,midg; midg,igrid,midg 6.0663528E-09 2.7506882E-08 1,midg,midg; igrid,midg,midg 1.4322365E-08 1.5039086E-08 gauss-seidel spectral radius is 0.9873127 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 00:05:24 rms-change max change #iterations 0.1315019 20.45723 at 10iterations 1.2972984E-02 1.968791 at 20iterations 1.2685439E-03 0.1950724 at 30iterations 1.2581043E-04 1.8547058E-02 at 40iterations 1.2499306E-05 2.0680428E-03 at 50iterations finished qdiffx linear iterations at : 00:05:27 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.2499306E-05 2.0680428E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 00:05:27 3.375u 0.175s 0:03.86 91.7% 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 Sun Oct 9 2011 at 00:05:27 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2248 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918724 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): 0.4799999 53.56700 ymin,ymax (A): 8.077000 51.51500 zmin,zma (A): -7.521000 48.14100 x,y,z range (A): 53.08700 43.43800 55.66200 scale (grids/A): 1.918724 object centre (A): 27.02350 29.79600 20.31000 number of atom coordinates read : 2248 total number of charged atoms : 2114 net assigned charge : 10.51402 assigned positive charge : 327.8566 centred at (gu) : 87.22929 92.69347 88.13350 assigned negative charge : -317.3432 centred at (gu) : 87.12836 92.44653 88.14365 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22020 grid for indexing accessible points = 1.400000 m= 24130 mr = 44433 m= 3836 mr = 17066 m= 226 mr = 2231 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 31762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 16650 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) : 0.6395745 object centre at (A) : 27.02350 29.79600 20.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8790236E-02 5.2196991E-02 midg,1,midg; midg,igrid,midg -3.0322310E-03 2.4214700E-02 1,midg,midg; igrid,midg,midg 4.7178905E-02 4.0098272E-02 gauss-seidel spectral radius is 0.9986289 estimated iterations to convergence 214 setup time was (sec) 0.5500000 now iterating at: 00:05:28 rms-change max change #iterations 3.869407 189.9881 at 10iterations 1.800656 71.05740 at 20iterations 0.8395358 29.49959 at 30iterations 0.3902937 13.07732 at 40iterations 0.1825308 6.518909 at 50iterations 8.5109286E-02 2.842567 at 60iterations 3.9563455E-02 1.341354 at 70iterations 1.8530790E-02 0.5941334 at 80iterations 8.6576743E-03 0.3101635 at 90iterations 4.0438282E-03 0.1405237 at 100iterations 1.8858514E-03 6.2919140E-02 at 110iterations 8.8240753E-04 3.2638550E-02 at 120iterations finished qdiffx linear iterations at : 00:05:35 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 8.8240753E-04 3.2638550E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 00:05:35 7.754u 0.218s 0:08.22 96.8% 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 Sun Oct 9 2011 at 00:05:36 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2248 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.878085 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): 0.4799999 53.56700 ymin,ymax (A): 8.077000 51.51500 zmin,zma (A): -7.521000 48.14100 x,y,z range (A): 53.08700 43.43800 55.66200 scale (grids/A): 2.878085 object centre (A): 27.02350 29.79600 20.31000 number of atom coordinates read : 2248 total number of charged atoms : 2114 net assigned charge : 10.51402 assigned positive charge : 327.8566 centred at (gu) : 85.84375 94.04019 87.20040 assigned negative charge : -317.3432 centred at (gu) : 85.69260 93.66984 87.21553 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 155429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22020 grid for indexing accessible points = 1.400000 m= 77154 mr = 108128 m= 28154 mr = 61415 m= 6674 mr = 21889 m= 946 mr = 4688 m= 43 mr = 568 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 71702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 16911 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) : 1.918724 object centre at (A) : 27.02350 29.79600 20.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2044111 0.6558818 midg,1,midg; midg,igrid,midg -1.8464809E-02 0.2372175 1,midg,midg; igrid,midg,midg 0.4115689 0.4143986 gauss-seidel spectral radius is 0.9992599 estimated iterations to convergence 290 setup time was (sec) 1.120000 now iterating at: 00:05:37 rms-change max change #iterations 9.240141 345.5984 at 10iterations 5.437202 133.1507 at 20iterations 3.166411 89.86701 at 30iterations 1.839049 46.05320 at 40iterations 1.067834 23.66162 at 50iterations 0.6154264 11.75606 at 60iterations 0.3556253 7.099777 at 70iterations 0.2049929 4.214912 at 80iterations 0.1181683 2.326002 at 90iterations 6.7793354E-02 1.379607 at 100iterations 3.9062232E-02 0.7383599 at 110iterations 2.2482004E-02 0.4702759 at 120iterations 1.2908443E-02 0.2411346 at 130iterations 7.4020051E-03 0.1354656 at 140iterations 4.2538946E-03 8.0749512E-02 at 150iterations 2.4455518E-03 4.7554970E-02 at 160iterations 1.4035585E-03 2.5802612E-02 at 170iterations 8.0488634E-04 1.5333176E-02 at 180iterations finished qdiffx linear iterations at : 00:05:48 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 8.0488634E-04 1.5333176E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 00:05:49 12.605u 0.208s 0:13.07 97.9% 0+0k 0+0io 0pf+0w