Sun Oct 9 08:21:40 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 08:21:40 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5179086 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): 14.92700 81.19800 ymin,ymax (A): 17.88800 84.45100 zmin,zma (A): 0.2020000 68.93999 x,y,z range (A): 66.27100 66.56300 68.73799 scale (grids/A): 0.5179086 object centre (A): 48.06250 51.16950 34.57100 number of atom coordinates read : 5761 total number of charged atoms : 5595 net assigned charge : 2.000058 assigned positive charge : 869.8554 centred at (gu) : 90.54697 89.35067 90.06084 assigned negative charge : -867.8629 centred at (gu) : 90.51371 89.39729 90.24274 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 9869 nv = 96 ne = 84 npr = 115127 no. pairs analyzed = 115127 no. exposed pairs = 7428 no. arc points = 50681 no. surface atoms = 2480 nbur = 3281 mkacc time = 0.3300000 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 = 1.652000 m= 409 mr = 5100 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 5167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5084 ## 736 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 13255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8732598E-10 -7.7378770E-10 midg,1,midg; midg,igrid,midg 2.8105199E-10 -1.3729450E-10 1,midg,midg; igrid,midg,midg -9.0927439E-11 2.0798936E-10 gauss-seidel spectral radius is 0.9810045 estimated iterations to convergence 60 setup time was (sec) 0.9300000 now iterating at: 08:21:41 rms-change max change #iterations 8.0754228E-02 11.38549 at 10iterations 4.9771643E-03 0.7040920 at 20iterations 5.8627361E-04 0.1199455 at 30iterations 1.6831218E-04 3.5850525E-02 at 40iterations 5.6177709E-05 1.1461258E-02 at 50iterations finished qdiffx linear iterations at : 08:21:45 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 5.6177709E-05 1.1461258E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 08:21:45 4.407u 0.248s 0:04.93 94.1% 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 08:21:45 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.553726 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): 14.92700 81.19800 ymin,ymax (A): 17.88800 84.45100 zmin,zma (A): 0.2020000 68.93999 x,y,z range (A): 66.27100 66.56300 68.73799 scale (grids/A): 1.553726 object centre (A): 48.06250 51.16950 34.57100 number of atom coordinates read : 5761 total number of charged atoms : 5595 net assigned charge : 2.000058 assigned positive charge : 869.8554 centred at (gu) : 91.63930 88.05032 90.18091 assigned negative charge : -867.8629 centred at (gu) : 91.54128 88.19160 90.72812 start vw surface at 0.2500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 109806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50681 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 34312 mr = 74824 m= 3257 mr = 22952 m= 75 mr = 1406 m= 0 mr = 3 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 787 time to turn everything in is 0.9900000 number of dielectric boundary points 48265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 755 ## 8 charges are in solution ## iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 42261 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) : 0.5179086 object centre at (A) : 48.06250 51.16950 34.57100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6678970E-02 -4.1994482E-02 midg,1,midg; midg,igrid,midg 9.0007536E-04 -1.6826320E-02 1,midg,midg; igrid,midg,midg 5.8175349E-03 2.6297774E-03 gauss-seidel spectral radius is 0.9982657 estimated iterations to convergence 191 setup time was (sec) 1.300000 now iterating at: 08:21:47 rms-change max change #iterations 4.372890 182.6133 at 10iterations 1.856616 70.21483 at 20iterations 0.7893596 22.63263 at 30iterations 0.3352557 11.56676 at 40iterations 0.1427010 4.226927 at 50iterations 6.0850795E-02 1.708103 at 60iterations 2.5993096E-02 0.7980804 at 70iterations 1.1104152E-02 0.3199577 at 80iterations 4.7603422E-03 0.1374474 at 90iterations 2.0677852E-03 6.0762405E-02 at 100iterations 9.1476098E-04 3.0098200E-02 at 110iterations 4.2414683E-04 1.6685486E-02 at 120iterations finished qdiffx linear iterations at : 08:21:55 total time elapsed so far: 9.900000 # loops : 120 mean,max change (kT/e) : 4.2414683E-04 1.6685486E-02 energy calculations done at 9.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.08000 DelPhi exited at 08:21:56 10.083u 0.290s 0:10.66 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 Sun Oct 9 2011 at 08:21:56 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5761 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.330589 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): 14.92700 81.19800 ymin,ymax (A): 17.88800 84.45100 zmin,zma (A): 0.2020000 68.93999 x,y,z range (A): 66.27100 66.56300 68.73799 scale (grids/A): 2.330589 object centre (A): 48.06250 51.16950 34.57100 number of atom coordinates read : 5761 total number of charged atoms : 5595 net assigned charge : 2.000058 assigned positive charge : 869.8554 centred at (gu) : 92.45856 87.07485 90.27096 assigned negative charge : -867.8629 centred at (gu) : 92.31176 87.28734 91.09207 start vw surface at 0.2500000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 254952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50681 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 119433 mr = 183580 m= 33210 mr = 92881 m= 4858 mr = 24264 m= 242 mr = 2973 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 1.530000 no. cavity mid-points inaccessible to solvent = 2545 time to turn everything in is 2.470000 number of dielectric boundary points 108944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 2.630000 number of grid points assigned charge 44638 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) : 1.553726 object centre at (A) : 48.06250 51.16950 34.57100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4252380 -0.9181701 midg,1,midg; midg,igrid,midg -2.8925091E-02 -0.3330605 1,midg,midg; igrid,midg,midg 0.1677834 0.1565204 gauss-seidel spectral radius is 0.9992376 estimated iterations to convergence 286 setup time was (sec) 2.810000 now iterating at: 08:21:59 rms-change max change #iterations 11.82800 435.2340 at 10iterations 7.016106 145.4969 at 20iterations 4.131876 92.46400 at 30iterations 2.414478 54.37294 at 40iterations 1.405489 28.53479 at 50iterations 0.8164480 16.06450 at 60iterations 0.4728051 8.250662 at 70iterations 0.2725805 5.056547 at 80iterations 0.1574376 2.637962 at 90iterations 9.0428360E-02 1.423050 at 100iterations 5.2097559E-02 0.8861732 at 110iterations 2.9904585E-02 0.5054131 at 120iterations 1.7218975E-02 0.2979584 at 130iterations 9.8682642E-03 0.1579285 at 140iterations 5.6764060E-03 9.5642090E-02 at 150iterations 3.2664712E-03 5.8077812E-02 at 160iterations 1.8813113E-03 3.4175873E-02 at 170iterations 1.0906975E-03 1.8943787E-02 at 180iterations finished qdiffx linear iterations at : 08:22:13 total time elapsed so far: 17.47000 # loops : 180 mean,max change (kT/e) : 1.0906975E-03 1.8943787E-02 energy calculations done at 17.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.65000 DelPhi exited at 08:22:14 17.648u 0.316s 0:18.23 98.4% 0+0k 0+0io 0pf+0w