Sun Oct 9 00:27:24 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 Sun Oct 9 2011 at 00:27:24 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 = 2276 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: 0.6528636 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): 0.4529999 53.42100 ymin,ymax (A): 8.105000 51.42700 zmin,zma (A): -6.242000 48.28700 x,y,z range (A): 52.96800 43.32200 54.52900 scale (grids/A): 0.6528636 object centre (A): 26.93700 29.76600 21.02250 number of atom coordinates read : 2276 total number of charged atoms : 2142 net assigned charge : 9.500019 assigned positive charge : 329.8346 centred at (gu) : 89.55260 90.92300 88.92360 assigned negative charge : -320.3352 centred at (gu) : 89.56608 90.82967 88.89907 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6748 nv = 96 ne = 84 npr = 45548 no. pairs analyzed = 45548 no. exposed pairs = 3006 no. arc points = 21859 no. surface atoms = 1008 nbur = 1268 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3534 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2058 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7824 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0374229E-08 1.8526748E-08 midg,1,midg; midg,igrid,midg 5.8965988E-09 3.9094704E-08 1,midg,midg; igrid,midg,midg 2.3620197E-08 1.6368492E-08 gauss-seidel spectral radius is 0.9878210 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 00:27:25 rms-change max change #iterations 0.1418829 22.78959 at 10iterations 1.4548489E-02 1.919990 at 20iterations 1.5135575E-03 0.2156525 at 30iterations 1.7163268E-04 2.5800705E-02 at 40iterations 2.6048561E-05 4.5442581E-03 at 50iterations finished qdiffx linear iterations at : 00:27:29 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 2.6048561E-05 4.5442581E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 00:27:30 4.433u 0.417s 0:05.21 92.8% 0+0k 0+0io 6pf+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 00:27:30 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 = 2276 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: 1.958591 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): 0.4529999 53.42100 ymin,ymax (A): 8.105000 51.42700 zmin,zma (A): -6.242000 48.28700 x,y,z range (A): 52.96800 43.32200 54.52900 scale (grids/A): 1.958591 object centre (A): 26.93700 29.76600 21.02250 number of atom coordinates read : 2276 total number of charged atoms : 2142 net assigned charge : 9.500019 assigned positive charge : 329.8346 centred at (gu) : 88.65765 92.76867 86.77049 assigned negative charge : -320.3352 centred at (gu) : 88.69828 92.48936 86.69732 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21859 grid for indexing accessible points = 1.400000 m= 25814 mr = 47753 m= 4285 mr = 18607 m= 280 mr = 2593 m= 5 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 32808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 16940 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) : 0.6528636 object centre at (A) : 26.93700 29.76600 21.02250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9728115E-02 5.2206844E-02 midg,1,midg; midg,igrid,midg -2.4878336E-03 2.9753460E-02 1,midg,midg; igrid,midg,midg 5.3177562E-02 4.7569480E-02 gauss-seidel spectral radius is 0.9986836 estimated iterations to convergence 218 setup time was (sec) 0.9100000 now iterating at: 00:27:31 rms-change max change #iterations 4.032444 181.9487 at 10iterations 1.910414 68.07089 at 20iterations 0.9035159 31.19577 at 30iterations 0.4306638 14.11265 at 40iterations 0.2037115 7.602057 at 50iterations 9.6408077E-02 3.083071 at 60iterations 4.5678336E-02 1.479210 at 70iterations 2.1678319E-02 0.7580833 at 80iterations 1.0253252E-02 0.3824234 at 90iterations 4.9076607E-03 0.1639739 at 100iterations 2.3289160E-03 6.9766998E-02 at 110iterations 1.1034145E-03 3.4393311E-02 at 120iterations finished qdiffx linear iterations at : 00:27:41 total time elapsed so far: 10.58000 # loops : 120 mean,max change (kT/e) : 1.1034145E-03 3.4393311E-02 energy calculations done at 10.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.75000 DelPhi exited at 00:27:41 10.750u 0.481s 0:11.49 97.7% 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 00:27:41 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 = 2276 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: 2.937886 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): 0.4529999 53.42100 ymin,ymax (A): 8.105000 51.42700 zmin,zma (A): -6.242000 48.28700 x,y,z range (A): 52.96800 43.32200 54.52900 scale (grids/A): 2.937886 object centre (A): 26.93700 29.76600 21.02250 number of atom coordinates read : 2276 total number of charged atoms : 2142 net assigned charge : 9.500019 assigned positive charge : 329.8346 centred at (gu) : 87.98644 94.15301 85.15572 assigned negative charge : -320.3352 centred at (gu) : 88.04753 93.73399 85.04597 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 164853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21859 grid for indexing accessible points = 1.400000 m= 82492 mr = 116274 m= 30803 mr = 65999 m= 7665 mr = 24314 m= 1211 mr = 5644 m= 82 mr = 828 m= 5 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 74030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 17136 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) : 1.958591 object centre at (A) : 26.93700 29.76600 21.02250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2641441 0.7489024 midg,1,midg; midg,igrid,midg -6.0156663E-03 0.2705296 1,midg,midg; igrid,midg,midg 0.4761640 0.5441273 gauss-seidel spectral radius is 0.9992789 estimated iterations to convergence 294 setup time was (sec) 1.870000 now iterating at: 00:27:44 rms-change max change #iterations 9.543170 413.9280 at 10iterations 5.662144 136.9507 at 20iterations 3.353170 80.43439 at 30iterations 1.973697 43.14308 at 40iterations 1.155011 23.23524 at 50iterations 0.6746897 14.56552 at 60iterations 0.3942879 9.350952 at 70iterations 0.2290728 4.473740 at 80iterations 0.1335363 2.485905 at 90iterations 7.7270776E-02 1.374863 at 100iterations 4.4974856E-02 0.9267812 at 110iterations 2.6113454E-02 0.4876623 at 120iterations 1.5119611E-02 0.2875900 at 130iterations 8.7689599E-03 0.1650009 at 140iterations 5.0755166E-03 0.1003556 at 150iterations 2.9392426E-03 5.6213379E-02 at 160iterations 1.7064692E-03 3.0030489E-02 at 170iterations 9.8637224E-04 1.8901348E-02 at 180iterations finished qdiffx linear iterations at : 00:28:00 total time elapsed so far: 17.84000 # loops : 180 mean,max change (kT/e) : 9.8637224E-04 1.8901348E-02 energy calculations done at 17.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.01000 DelPhi exited at 00:28:00 18.011u 0.474s 0:18.77 98.4% 0+0k 0+0io 0pf+0w