Mon Oct 10 14:07:48 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 Mon Oct 10 2011 at 14:07:48 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 = 2272 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: 0.6839052 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): -20.46700 31.58700 ymin,ymax (A): -58.39700 -12.54500 zmin,zma (A): -8.220000 42.19100 x,y,z range (A): 52.05400 45.85201 50.41100 scale (grids/A): 0.6839052 object centre (A): 5.560000 -35.47100 16.98550 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -3.499991 assigned positive charge : 340.7924 centred at (gu) : 89.29975 89.24201 89.56966 assigned negative charge : -344.2929 centred at (gu) : 89.47057 89.23920 89.50909 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7463 nv = 96 ne = 84 npr = 45463 no. pairs analyzed = 45463 no. exposed pairs = 3031 no. arc points = 21060 no. surface atoms = 1037 nbur = 1235 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4078 m= 8 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1925 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9448732E-08 1.9357078E-09 midg,1,midg; midg,igrid,midg -2.0600268E-08 -1.3811218E-08 1,midg,midg; igrid,midg,midg 4.2109992E-08 -6.2442830E-08 gauss-seidel spectral radius is 0.9888947 estimated iterations to convergence 77 setup time was (sec) 0.5400000 now iterating at: 14:07:49 rms-change max change #iterations 0.1821769 30.76106 at 10iterations 2.1066964E-02 3.025181 at 20iterations 2.4176762E-03 0.3504524 at 30iterations 2.8211402E-04 3.9106369E-02 at 40iterations 3.3221491E-05 4.3478012E-03 at 50iterations finished qdiffx linear iterations at : 14:07:52 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 3.3221491E-05 4.3478012E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:07:52 3.313u 0.156s 0:03.80 91.0% 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 14:07:52 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 = 2272 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: 2.051715 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): -20.46700 31.58700 ymin,ymax (A): -58.39700 -12.54500 zmin,zma (A): -8.220000 42.19100 x,y,z range (A): 52.05400 45.85201 50.41100 scale (grids/A): 2.051715 object centre (A): 5.560000 -35.47100 16.98550 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -3.499991 assigned positive charge : 340.7924 centred at (gu) : 87.89893 87.72575 88.70872 assigned negative charge : -344.2929 centred at (gu) : 88.41153 87.71762 88.52705 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21060 grid for indexing accessible points = 1.400000 m= 31004 mr = 54231 m= 6175 mr = 23030 m= 559 mr = 4057 m= 24 mr = 247 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 35304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 16975 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) : 0.6839052 object centre at (A) : 5.560000 -35.47100 16.98550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3766640E-02 -2.6172234E-02 midg,1,midg; midg,igrid,midg -2.5745828E-03 -8.5660564E-03 1,midg,midg; igrid,midg,midg -1.1665197E-03 -8.0399094E-03 gauss-seidel spectral radius is 0.9987956 estimated iterations to convergence 228 setup time was (sec) 0.8500000 now iterating at: 14:07:53 rms-change max change #iterations 4.610431 224.0364 at 10iterations 2.238731 80.70407 at 20iterations 1.102007 32.07987 at 30iterations 0.5383957 15.44918 at 40iterations 0.2643954 8.452835 at 50iterations 0.1292452 4.026787 at 60iterations 6.3541293E-02 2.040615 at 70iterations 3.1082675E-02 0.8563652 at 80iterations 1.5207869E-02 0.4242153 at 90iterations 7.4843317E-03 0.2176011 at 100iterations 3.6830413E-03 0.1162453 at 110iterations 1.7993073E-03 5.5550575E-02 at 120iterations finished qdiffx linear iterations at : 14:08:00 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 1.7993073E-03 5.5550575E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 14:08:01 7.599u 0.269s 0:08.40 93.4% 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 Mon Oct 10 2011 at 14:08:01 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2272 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: 3.077573 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): -20.46700 31.58700 ymin,ymax (A): -58.39700 -12.54500 zmin,zma (A): -8.220000 42.19100 x,y,z range (A): 52.05400 45.85201 50.41100 scale (grids/A): 3.077573 object centre (A): 5.560000 -35.47100 16.98550 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -3.499991 assigned positive charge : 340.7924 centred at (gu) : 86.84830 86.58857 88.06303 assigned negative charge : -344.2929 centred at (gu) : 87.61729 86.57635 87.79058 start vw surface at 0.1200000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 182673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21060 grid for indexing accessible points = 1.400000 m= 96249 mr = 131505 m= 39597 mr = 78972 m= 11677 mr = 31930 m= 2337 mr = 8911 m= 238 mr = 1649 m= 15 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.790000 number of dielectric boundary points 79716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 17112 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) : 2.051715 object centre at (A) : 5.560000 -35.47100 16.98550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2411628 -0.5434946 midg,1,midg; midg,igrid,midg 7.9653122E-02 8.5310210E-03 1,midg,midg; igrid,midg,midg -0.3835551 -2.1987823E-03 gauss-seidel spectral radius is 0.9992995 estimated iterations to convergence 298 setup time was (sec) 2.110000 now iterating at: 14:08:03 rms-change max change #iterations 10.59893 453.7473 at 10iterations 6.328891 162.1985 at 20iterations 3.768526 73.97853 at 30iterations 2.238061 40.64538 at 40iterations 1.323897 24.22716 at 50iterations 0.7825681 15.74199 at 60iterations 0.4601539 9.459475 at 70iterations 0.2706529 4.615395 at 80iterations 0.1587407 2.782595 at 90iterations 9.2969894E-02 1.754890 at 100iterations 5.4464016E-02 0.9660568 at 110iterations 3.1856421E-02 0.5835915 at 120iterations 1.8639317E-02 0.3223758 at 130iterations 1.0881244E-02 0.1802349 at 140iterations 6.3846200E-03 0.1123123 at 150iterations 3.7357213E-03 6.5995216E-02 at 160iterations 2.1890602E-03 3.6071777E-02 at 170iterations 1.2862333E-03 2.2634506E-02 at 180iterations finished qdiffx linear iterations at : 14:08:14 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.2862333E-03 2.2634506E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 14:08:14 12.868u 0.273s 0:13.62 96.4% 0+0k 0+0io 0pf+0w