Mon Oct 10 14:41:55 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 Mon Oct 10 2011 at 14:41:56 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 = 2423 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: 0.6079858 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): -5.372000 46.35100 ymin,ymax (A): -25.43900 33.11500 zmin,zma (A): 9.250000 64.20200 x,y,z range (A): 51.72300 58.55400 54.95200 scale (grids/A): 0.6079858 object centre (A): 20.48950 3.838001 36.72600 number of atom coordinates read : 2423 total number of charged atoms : 2278 net assigned charge : -1.999993 assigned positive charge : 354.6772 centred at (gu) : 88.47770 90.71863 89.36195 assigned negative charge : -356.6777 centred at (gu) : 88.32933 90.60252 89.32404 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5962 nv = 96 ne = 84 npr = 48985 no. pairs analyzed = 48985 no. exposed pairs = 3233 no. arc points = 22878 no. surface atoms = 1096 nbur = 1327 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 269 mr = 3020 m= 0 mr = 12 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2254 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7353 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0463081E-09 5.0723609E-10 midg,1,midg; midg,igrid,midg -5.1311595E-09 4.5764699E-09 1,midg,midg; igrid,midg,midg -1.0562601E-08 3.6758383E-09 gauss-seidel spectral radius is 0.9859850 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 14:41:56 rms-change max change #iterations 0.1065139 25.40582 at 10iterations 9.2459843E-03 1.592236 at 20iterations 8.1741548E-04 0.1343689 at 30iterations 7.1768889E-05 1.3092041E-02 at 40iterations 6.2374584E-06 9.6672773E-04 at 50iterations finished qdiffx linear iterations at : 14:42:00 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 6.2374584E-06 9.6672773E-04 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 14:42:01 4.521u 0.371s 0:05.31 92.0% 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 Mon Oct 10 2011 at 14:42:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.823957 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): -5.372000 46.35100 ymin,ymax (A): -25.43900 33.11500 zmin,zma (A): 9.250000 64.20200 x,y,z range (A): 51.72300 58.55400 54.95200 scale (grids/A): 1.823957 object centre (A): 20.48950 3.838001 36.72600 number of atom coordinates read : 2423 total number of charged atoms : 2278 net assigned charge : -1.999993 assigned positive charge : 354.6772 centred at (gu) : 85.43256 92.15549 88.08551 assigned negative charge : -356.6777 centred at (gu) : 84.98783 91.80746 87.97205 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22878 grid for indexing accessible points = 1.400000 m= 21080 mr = 42972 m= 2701 mr = 14414 m= 103 mr = 1412 m= 0 mr = 15 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 29557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17817 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) : 0.6079858 object centre at (A) : 20.48950 3.838001 36.72600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9079670E-02 2.8229069E-03 midg,1,midg; midg,igrid,midg -1.9293913E-03 3.4105002E-03 1,midg,midg; igrid,midg,midg -7.0010284E-03 8.0747148E-03 gauss-seidel spectral radius is 0.9984937 estimated iterations to convergence 204 setup time was (sec) 0.8500000 now iterating at: 14:42:02 rms-change max change #iterations 3.708499 204.4197 at 10iterations 1.659016 65.24564 at 20iterations 0.7484406 29.23318 at 30iterations 0.3368511 12.10476 at 40iterations 0.1520142 5.940746 at 50iterations 6.8230703E-02 2.414051 at 60iterations 3.0746927E-02 1.006935 at 70iterations 1.3826833E-02 0.5043488 at 80iterations 6.2379199E-03 0.2331009 at 90iterations 2.8031901E-03 9.5581055E-02 at 100iterations 1.2689689E-03 4.9357414E-02 at 110iterations 5.7233748E-04 1.9865513E-02 at 120iterations finished qdiffx linear iterations at : 14:42:12 total time elapsed so far: 10.35000 # loops : 120 mean,max change (kT/e) : 5.7233748E-04 1.9865513E-02 energy calculations done at 10.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.51000 DelPhi exited at 14:42:12 10.510u 0.441s 0:11.26 97.2% 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 Mon Oct 10 2011 at 14:42:12 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 = 2423 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: 2.735936 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): -5.372000 46.35100 ymin,ymax (A): -25.43900 33.11500 zmin,zma (A): 9.250000 64.20200 x,y,z range (A): 51.72300 58.55400 54.95200 scale (grids/A): 2.735936 object centre (A): 20.48950 3.838001 36.72600 number of atom coordinates read : 2423 total number of charged atoms : 2278 net assigned charge : -1.999993 assigned positive charge : 354.6772 centred at (gu) : 83.14874 93.23318 87.12823 assigned negative charge : -356.6777 centred at (gu) : 82.48181 92.71120 86.95805 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 149165 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22878 grid for indexing accessible points = 1.400000 m= 69826 mr = 104531 m= 22760 mr = 55032 m= 4527 mr = 17279 m= 496 mr = 2954 m= 18 mr = 237 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 66760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 18218 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) : 1.823957 object centre at (A) : 20.48950 3.838001 36.72600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7022039 0.1545732 midg,1,midg; midg,igrid,midg 1.0726713E-02 7.4429937E-02 1,midg,midg; igrid,midg,midg -3.1379215E-02 7.7507697E-02 gauss-seidel spectral radius is 0.9992182 estimated iterations to convergence 282 setup time was (sec) 1.740000 now iterating at: 14:42:14 rms-change max change #iterations 8.857706 322.8388 at 10iterations 5.099438 110.4829 at 20iterations 2.908838 76.93437 at 30iterations 1.662529 36.65297 at 40iterations 0.9459934 21.39550 at 50iterations 0.5373328 11.37858 at 60iterations 0.3051285 6.328148 at 70iterations 0.1727319 3.507446 at 80iterations 9.7994275E-02 1.977015 at 90iterations 5.5268835E-02 1.312691 at 100iterations 3.1386681E-02 0.6196957 at 110iterations 1.7741306E-02 0.3639145 at 120iterations 1.0029887E-02 0.2068710 at 130iterations 5.6749335E-03 0.1107812 at 140iterations 3.2158266E-03 7.1098804E-02 at 150iterations 1.8100255E-03 3.5559654E-02 at 160iterations 1.0242672E-03 2.1077156E-02 at 170iterations 5.7965156E-04 1.1566162E-02 at 180iterations finished qdiffx linear iterations at : 14:42:30 total time elapsed so far: 17.45000 # loops : 180 mean,max change (kT/e) : 5.7965156E-04 1.1566162E-02 energy calculations done at 17.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.61000 DelPhi exited at 14:42:31 17.616u 0.450s 0:18.70 96.5% 0+0k 0+0io 0pf+0w