Sun Oct 9 00:41:20 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 Sun Oct 9 2011 at 00:41:20 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 = 2267 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: 0.6510964 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): -0.8740000 53.80300 ymin,ymax (A): -15.62900 27.45900 zmin,zma (A): 32.24500 83.99500 x,y,z range (A): 54.67700 43.08800 51.75000 scale (grids/A): 0.6510964 object centre (A): 26.46450 5.915000 58.12000 number of atom coordinates read : 2267 total number of charged atoms : 2133 net assigned charge : 10.50002 assigned positive charge : 327.9037 centred at (gu) : 90.63355 88.84052 88.28987 assigned negative charge : -317.4042 centred at (gu) : 90.61515 88.93701 88.29984 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6608 nv = 96 ne = 84 npr = 45746 no. pairs analyzed = 45746 no. exposed pairs = 2992 no. arc points = 21265 no. surface atoms = 1006 nbur = 1261 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 338 mr = 3414 m= 3 mr = 28 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 0.2700000 number of dielectric boundary points 3507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2050 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1123122E-08 1.3732503E-08 midg,1,midg; midg,igrid,midg 4.1818545E-08 6.5881660E-09 1,midg,midg; igrid,midg,midg 1.6078209E-08 2.6147870E-08 gauss-seidel spectral radius is 0.9877524 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 00:41:21 rms-change max change #iterations 0.1396148 21.14182 at 10iterations 1.4226667E-02 2.043395 at 20iterations 1.4519291E-03 0.1970596 at 30iterations 1.6858285E-04 2.4203300E-02 at 40iterations 2.8535731E-05 4.6236515E-03 at 50iterations finished qdiffx linear iterations at : 00:41:24 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 2.8535731E-05 4.6236515E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 00:41:25 4.193u 0.274s 0:04.73 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 00:41:25 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 = 2267 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: 1.953289 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): -0.8740000 53.80300 ymin,ymax (A): -15.62900 27.45900 zmin,zma (A): 32.24500 83.99500 x,y,z range (A): 54.67700 43.08800 51.75000 scale (grids/A): 1.953289 object centre (A): 26.46450 5.915000 58.12000 number of atom coordinates read : 2267 total number of charged atoms : 2133 net assigned charge : 10.50002 assigned positive charge : 327.9037 centred at (gu) : 91.90042 86.52139 84.86941 assigned negative charge : -317.4042 centred at (gu) : 91.84564 86.81091 84.89981 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70167 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21265 grid for indexing accessible points = 1.400000 m= 24821 mr = 47083 m= 4011 mr = 17688 m= 258 mr = 2368 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.5400000 number of dielectric boundary points 32041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 16825 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) : 0.6510964 object centre at (A) : 26.46450 5.915000 58.12000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0458460E-02 3.5826843E-02 midg,1,midg; midg,igrid,midg 3.4903165E-02 -3.9522424E-03 1,midg,midg; igrid,midg,midg 4.4486087E-02 6.3683756E-02 gauss-seidel spectral radius is 0.9986712 estimated iterations to convergence 217 setup time was (sec) 0.8700000 now iterating at: 00:41:26 rms-change max change #iterations 3.969758 190.1442 at 10iterations 1.869035 73.64636 at 20iterations 0.8826944 37.06000 at 30iterations 0.4167891 13.76942 at 40iterations 0.1968976 5.906115 at 50iterations 9.2808902E-02 2.959211 at 60iterations 4.3870158E-02 1.517391 at 70iterations 2.0899449E-02 0.6753268 at 80iterations 9.8396419E-03 0.3247204 at 90iterations 4.6516829E-03 0.1537247 at 100iterations 2.2029283E-03 7.3745728E-02 at 110iterations 1.0538230E-03 3.1829834E-02 at 120iterations finished qdiffx linear iterations at : 00:41:34 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 1.0538230E-03 3.1829834E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 00:41:35 9.605u 0.303s 0:10.20 97.0% 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 Sun Oct 9 2011 at 00:41:35 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 = 2267 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: 2.929934 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): -0.8740000 53.80300 ymin,ymax (A): -15.62900 27.45900 zmin,zma (A): 32.24500 83.99500 x,y,z range (A): 54.67700 43.08800 51.75000 scale (grids/A): 2.929934 object centre (A): 26.46450 5.915000 58.12000 number of atom coordinates read : 2267 total number of charged atoms : 2133 net assigned charge : 10.50002 assigned positive charge : 327.9037 centred at (gu) : 92.85058 84.78202 82.30418 assigned negative charge : -317.4042 centred at (gu) : 92.76846 85.21642 82.34977 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 162166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21265 grid for indexing accessible points = 1.400000 m= 79247 mr = 114345 m= 28806 mr = 63320 m= 7289 mr = 22673 m= 1093 mr = 5271 m= 63 mr = 692 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 982 time to turn everything in is 1.390000 number of dielectric boundary points 72339 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 17064 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) : 1.953289 object centre at (A) : 26.46450 5.915000 58.12000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3078061 0.4957319 midg,1,midg; midg,igrid,midg 0.3251401 -3.0069269E-02 1,midg,midg; igrid,midg,midg 0.5262040 0.5775366 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 1.740000 now iterating at: 00:41:37 rms-change max change #iterations 9.477724 299.1570 at 10iterations 5.613067 133.7493 at 20iterations 3.305329 71.68106 at 30iterations 1.931183 48.44740 at 40iterations 1.129486 23.56906 at 50iterations 0.6577857 13.69461 at 60iterations 0.3825100 8.469933 at 70iterations 0.2222482 4.753508 at 80iterations 0.1287295 2.292114 at 90iterations 7.4682258E-02 1.439445 at 100iterations 4.3354966E-02 0.7938995 at 110iterations 2.5087729E-02 0.4702644 at 120iterations 1.4506699E-02 0.2917824 at 130iterations 8.3958097E-03 0.1749611 at 140iterations 4.8660636E-03 0.1012726 at 150iterations 2.8077355E-03 5.4164410E-02 at 160iterations 1.6288081E-03 2.9734612E-02 at 170iterations 9.4412756E-04 1.8421918E-02 at 180iterations finished qdiffx linear iterations at : 00:41:51 total time elapsed so far: 15.43000 # loops : 180 mean,max change (kT/e) : 9.4412756E-04 1.8421918E-02 energy calculations done at 15.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.60000 DelPhi exited at 00:41:51 15.605u 0.384s 0:16.29 98.0% 0+0k 0+0io 0pf+0w