Sat Oct 8 16:32:36 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 16:32:36 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5447340 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): 21.30600 78.90300 ymin,ymax (A): 118.8860 184.2390 zmin,zma (A): -1.775000 59.81700 x,y,z range (A): 57.59700 65.35300 61.59200 scale (grids/A): 0.5447340 object centre (A): 50.10450 151.5625 29.02100 number of atom coordinates read : 4503 total number of charged atoms : 4333 net assigned charge : 5.000041 assigned positive charge : 691.1336 centred at (gu) : 90.74308 89.49290 87.42093 assigned negative charge : -686.1370 centred at (gu) : 90.74268 89.44328 87.46264 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8586 nv = 96 ne = 84 npr = 90785 no. pairs analyzed = 90785 no. exposed pairs = 5515 no. arc points = 38379 no. surface atoms = 1848 nbur = 2655 mkacc time = 0.1500000 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= 388 mr = 4587 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3000000 number of dielectric boundary points 4370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3885 ## 499 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 11403 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3135962E-09 -5.9564673E-11 midg,1,midg; midg,igrid,midg -2.2873810E-10 6.7314360E-10 1,midg,midg; igrid,midg,midg 2.3520974E-10 3.4531805E-10 gauss-seidel spectral radius is 0.9827380 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 16:32:36 rms-change max change #iterations 9.0474173E-02 12.59527 at 10iterations 6.5624844E-03 0.9680328 at 20iterations 9.7346638E-04 0.1495972 at 30iterations 3.0459350E-04 4.6291351E-02 at 40iterations 1.0374462E-04 1.4980316E-02 at 50iterations finished qdiffx linear iterations at : 16:32:39 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.0374462E-04 1.4980316E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 16:32:40 3.601u 0.186s 0:04.07 92.8% 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 Sat Oct 8 2011 at 16:32:40 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.634202 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): 21.30600 78.90300 ymin,ymax (A): 118.8860 184.2390 zmin,zma (A): -1.775000 59.81700 x,y,z range (A): 57.59700 65.35300 61.59200 scale (grids/A): 1.634202 object centre (A): 50.10450 151.5625 29.02100 number of atom coordinates read : 4503 total number of charged atoms : 4333 net assigned charge : 5.000041 assigned positive charge : 691.1336 centred at (gu) : 92.22853 88.47762 82.26150 assigned negative charge : -686.1370 centred at (gu) : 92.22782 88.32966 82.38746 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 96627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38379 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30524 mr = 67459 m= 3467 mr = 20917 m= 117 mr = 1777 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1575 time to turn everything in is 0.4600000 number of dielectric boundary points 40571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 464 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33163 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) : 0.5447340 object centre at (A) : 50.10450 151.5625 29.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3040384E-03 8.9440458E-03 midg,1,midg; midg,igrid,midg 1.4571348E-02 3.3045191E-02 1,midg,midg; igrid,midg,midg -1.3873640E-02 -1.0595923E-02 gauss-seidel spectral radius is 0.9983394 estimated iterations to convergence 195 setup time was (sec) 0.6900000 now iterating at: 16:32:41 rms-change max change #iterations 4.279231 186.5647 at 10iterations 1.845933 57.83125 at 20iterations 0.7962605 26.11517 at 30iterations 0.3461402 10.70985 at 40iterations 0.1500874 4.436382 at 50iterations 6.5178998E-02 1.861114 at 60iterations 2.8244806E-02 0.8842783 at 70iterations 1.2330919E-02 0.4007378 at 80iterations 5.4092435E-03 0.1590958 at 90iterations 2.4252366E-03 7.0953369E-02 at 100iterations 1.1082453E-03 3.5460949E-02 at 110iterations 5.3619064E-04 1.7051697E-02 at 120iterations finished qdiffx linear iterations at : 16:32:48 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 5.3619064E-04 1.7051697E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 16:32:49 8.230u 0.223s 0:08.77 96.3% 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 16:32:49 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.451303 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): 21.30600 78.90300 ymin,ymax (A): 118.8860 184.2390 zmin,zma (A): -1.775000 59.81700 x,y,z range (A): 57.59700 65.35300 61.59200 scale (grids/A): 2.451303 object centre (A): 50.10450 151.5625 29.02100 number of atom coordinates read : 4503 total number of charged atoms : 4333 net assigned charge : 5.000041 assigned positive charge : 691.1336 centred at (gu) : 93.34231 87.71632 78.39196 assigned negative charge : -686.1370 centred at (gu) : 93.34164 87.49453 78.58119 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 224507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38379 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106337 mr = 165232 m= 31048 mr = 84216 m= 5589 mr = 23075 m= 485 mr = 3729 m= 13 mr = 254 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 5262 time to turn everything in is 1.180000 number of dielectric boundary points 91473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 34623 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) : 1.634202 object centre at (A) : 50.10450 151.5625 29.02100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0979950E-03 0.2047718 midg,1,midg; midg,igrid,midg 0.1888312 0.5895827 1,midg,midg; igrid,midg,midg -0.2214114 -0.1751118 gauss-seidel spectral radius is 0.9992179 estimated iterations to convergence 282 setup time was (sec) 1.450000 now iterating at: 16:32:50 rms-change max change #iterations 11.01049 362.8868 at 10iterations 6.396844 135.7746 at 20iterations 3.690858 73.45016 at 30iterations 2.121064 38.71137 at 40iterations 1.215679 27.25746 at 50iterations 0.6931476 13.64803 at 60iterations 0.3957289 6.987040 at 70iterations 0.2252415 4.086639 at 80iterations 0.1280252 2.176920 at 90iterations 7.2694704E-02 1.349919 at 100iterations 4.1206699E-02 0.7246217 at 110iterations 2.3412494E-02 0.4466858 at 120iterations 1.3257382E-02 0.2254868 at 130iterations 7.5218016E-03 0.1287575 at 140iterations 4.2758128E-03 7.6925755E-02 at 150iterations 2.4370821E-03 4.0850878E-02 at 160iterations 1.3932314E-03 2.5234222E-02 at 170iterations 8.0461521E-04 1.4781952E-02 at 180iterations finished qdiffx linear iterations at : 16:33:03 total time elapsed so far: 13.78000 # loops : 180 mean,max change (kT/e) : 8.0461521E-04 1.4781952E-02 energy calculations done at 13.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.92000 DelPhi exited at 16:33:03 13.919u 0.234s 0:14.45 97.8% 0+0k 0+0io 0pf+0w