Sun Oct 9 02:29:46 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 02:29:46 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: MG2 214 has a net charge of 1.4000 !!! WARNING: SAM 215 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 4 has a net charge of 0.4200 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: 0.7079083 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): -45.18300 5.106000 ymin,ymax (A): 49.93400 88.09700 zmin,zma (A): 23.30300 66.78500 x,y,z range (A): 50.28900 38.16300 43.48200 scale (grids/A): 0.7079083 object centre (A): -20.03850 69.01550 45.04400 number of atom coordinates read : 2013 total number of charged atoms : 1932 net assigned charge : -3.279994 assigned positive charge : 306.4268 centred at (gu) : 90.13869 89.29280 89.26503 assigned negative charge : -309.7072 centred at (gu) : 90.20565 89.31776 89.28520 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7099 nv = 96 ne = 84 npr = 40404 no. pairs analyzed = 40404 no. exposed pairs = 2261 no. arc points = 15839 no. surface atoms = 771 nbur = 1242 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4368 m= 3 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 294 time to turn everything in is 0.3000000 number of dielectric boundary points 3076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1434 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0687173E-08 -3.3129101E-08 midg,1,midg; midg,igrid,midg -1.7858541E-08 -3.5376868E-08 1,midg,midg; igrid,midg,midg 4.7189648E-09 -6.3176365E-08 gauss-seidel spectral radius is 0.9895941 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 02:29:47 rms-change max change #iterations 0.2040117 29.21338 at 10iterations 2.4649056E-02 3.188293 at 20iterations 3.0748907E-03 0.4438591 at 30iterations 3.7691320E-04 5.4626465E-02 at 40iterations 4.7214991E-05 6.8359375E-03 at 50iterations finished qdiffx linear iterations at : 02:29:50 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 4.7214991E-05 6.8359375E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 02:29:51 4.163u 0.294s 0:04.72 94.2% 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 Sun Oct 9 2011 at 02:29:51 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: MG2 214 has a net charge of 1.4000 !!! WARNING: SAM 215 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 4 has a net charge of 0.4200 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: 2.123725 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): -45.18300 5.106000 ymin,ymax (A): 49.93400 88.09700 zmin,zma (A): 23.30300 66.78500 x,y,z range (A): 50.28900 38.16300 43.48200 scale (grids/A): 2.123725 object centre (A): -20.03850 69.01550 45.04400 number of atom coordinates read : 2013 total number of charged atoms : 1932 net assigned charge : -3.279994 assigned positive charge : 306.4268 centred at (gu) : 90.41589 87.87805 87.79488 assigned negative charge : -309.7072 centred at (gu) : 90.61690 87.95332 87.85564 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 75736 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15839 grid for indexing accessible points = 1.400000 m= 32481 mr = 55606 m= 7303 mr = 26118 m= 747 mr = 5661 m= 15 mr = 484 m= 0 mr = 1 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 7388 time to turn everything in is 0.6700000 number of dielectric boundary points 28412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15376 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) : 0.7079083 object centre at (A) : -20.03850 69.01550 45.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9075971E-02 3.2624521E-03 midg,1,midg; midg,igrid,midg -2.3267450E-02 -1.2820393E-02 1,midg,midg; igrid,midg,midg -1.2458863E-02 1.1428390E-02 gauss-seidel spectral radius is 0.9988232 estimated iterations to convergence 231 setup time was (sec) 0.9800000 now iterating at: 02:29:52 rms-change max change #iterations 4.583980 173.3685 at 10iterations 2.258108 77.43842 at 20iterations 1.119781 34.11949 at 30iterations 0.5555359 17.97581 at 40iterations 0.2750914 8.911369 at 50iterations 0.1361952 4.898952 at 60iterations 6.7533672E-02 2.036777 at 70iterations 3.3388942E-02 1.017288 at 80iterations 1.6515343E-02 0.4738312 at 90iterations 8.1927339E-03 0.2574615 at 100iterations 4.0504797E-03 0.1346627 at 110iterations 2.0101264E-03 6.5988541E-02 at 120iterations finished qdiffx linear iterations at : 02:30:01 total time elapsed so far: 9.580000 # loops : 120 mean,max change (kT/e) : 2.0101264E-03 6.5988541E-02 energy calculations done at 9.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 02:30:01 9.767u 0.336s 0:10.46 96.4% 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 02:30:01 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: MG2 214 has a net charge of 1.4000 !!! WARNING: SAM 215 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 4 has a net charge of 0.4200 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: 3.185587 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): -45.18300 5.106000 ymin,ymax (A): 49.93400 88.09700 zmin,zma (A): 23.30300 66.78500 x,y,z range (A): 50.28900 38.16300 43.48200 scale (grids/A): 3.185587 object centre (A): -20.03850 69.01550 45.04400 number of atom coordinates read : 2013 total number of charged atoms : 1932 net assigned charge : -3.279994 assigned positive charge : 306.4268 centred at (gu) : 90.62381 86.81706 86.69234 assigned negative charge : -309.7072 centred at (gu) : 90.92537 86.93008 86.78342 start vw surface at 0.1400000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 174498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15839 grid for indexing accessible points = 1.400000 m= 98942 mr = 132931 m= 44141 mr = 85064 m= 14410 mr = 38304 m= 3249 mr = 12426 m= 403 mr = 2679 m= 20 mr = 271 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 25405 time to turn everything in is 2.180000 number of dielectric boundary points 63985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.340000 number of grid points assigned charge 15456 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) : 2.123725 object centre at (A) : -20.03850 69.01550 45.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3241361 0.1636668 midg,1,midg; midg,igrid,midg -0.1776342 -0.1042219 1,midg,midg; igrid,midg,midg -0.2042568 0.1256085 gauss-seidel spectral radius is 0.9992855 estimated iterations to convergence 295 setup time was (sec) 2.520000 now iterating at: 02:30:04 rms-change max change #iterations 10.06206 315.0276 at 10iterations 5.837897 110.8998 at 20iterations 3.386185 62.40850 at 30iterations 1.963225 35.71838 at 40iterations 1.139148 20.40203 at 50iterations 0.6623851 11.98009 at 60iterations 0.3832955 6.252563 at 70iterations 0.2224954 4.040733 at 80iterations 0.1286886 2.436394 at 90iterations 7.4738070E-02 1.404968 at 100iterations 4.3281533E-02 0.7088165 at 110iterations 2.5056278E-02 0.4501534 at 120iterations 1.4570780E-02 0.2481737 at 130iterations 8.4282598E-03 0.1535759 at 140iterations 4.8911409E-03 8.2183480E-02 at 150iterations 2.8371795E-03 4.7333598E-02 at 160iterations 1.6476773E-03 2.8404236E-02 at 170iterations 9.5313566E-04 1.7193556E-02 at 180iterations finished qdiffx linear iterations at : 02:30:18 total time elapsed so far: 16.63000 # loops : 180 mean,max change (kT/e) : 9.5313566E-04 1.7193556E-02 energy calculations done at 16.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.81000 DelPhi exited at 02:30:19 16.811u 0.346s 0:17.44 98.3% 0+0k 0+0io 0pf+0w