Mon Oct 10 11:07:14 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 11:07:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5402 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: 0.4877781 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 0.4877781 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 856.7913 centred at (gu) : 89.32052 90.44511 88.25726 assigned negative charge : -844.8000 centred at (gu) : 89.29486 90.49451 88.23253 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8120 nv = 96 ne = 84 npr = 106473 no. pairs analyzed = 106473 no. exposed pairs = 6506 no. arc points = 44171 no. surface atoms = 2193 nbur = 3209 mkacc time = 0.2500000 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 = 1.736000 m= 252 mr = 4337 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4292 ## 679 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0592672E-11 5.4221013E-11 midg,1,midg; midg,igrid,midg 1.0045887E-10 5.0263496E-12 1,midg,midg; igrid,midg,midg 3.7088818E-11 7.2882249E-11 gauss-seidel spectral radius is 0.9785555 estimated iterations to convergence 57 setup time was (sec) 0.7600000 now iterating at: 11:07:15 rms-change max change #iterations 5.7603028E-02 9.477276 at 10iterations 3.1188657E-03 0.5317402 at 20iterations 6.2810641E-04 9.8642349E-02 at 30iterations 3.0268010E-04 4.8437595E-02 at 40iterations 1.5169808E-04 2.4500370E-02 at 50iterations finished qdiffx linear iterations at : 11:07:18 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 1.5169808E-04 2.4500370E-02 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 11:07:19 3.838u 0.232s 0:04.37 92.9% 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 11:07:19 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5402 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: 1.463334 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 1.463334 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 856.7913 centred at (gu) : 87.95987 91.33338 84.76978 assigned negative charge : -844.8000 centred at (gu) : 87.88438 91.48367 84.69740 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 93556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44171 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 26239 mr = 66234 m= 1951 mr = 17503 m= 37 mr = 742 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1970 time to turn everything in is 0.7000000 number of dielectric boundary points 37304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 703 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 38804 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) : 0.4877781 object centre at (A) : -11.71000 5.882999 41.22550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6535955E-04 3.4864182E-03 midg,1,midg; midg,igrid,midg 8.5439691E-03 -2.4680424E-02 1,midg,midg; igrid,midg,midg 9.0403762E-04 1.5021172E-02 gauss-seidel spectral radius is 0.9979509 estimated iterations to convergence 176 setup time was (sec) 1.030000 now iterating at: 11:07:20 rms-change max change #iterations 3.753636 142.6780 at 10iterations 1.483289 48.68752 at 20iterations 0.5866227 20.95193 at 30iterations 0.2325619 7.071838 at 40iterations 9.1836482E-02 2.713272 at 50iterations 3.6392130E-02 1.184639 at 60iterations 1.4506695E-02 0.4581203 at 70iterations 5.8542322E-03 0.1888275 at 80iterations 2.4485504E-03 8.5769653E-02 at 90iterations 1.1547310E-03 4.3390274E-02 at 100iterations 6.7354226E-04 2.5198460E-02 at 110iterations 4.6732064E-04 1.7752171E-02 at 120iterations finished qdiffx linear iterations at : 11:07:27 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 4.6732064E-04 1.7752171E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 11:07:27 8.077u 0.246s 0:08.59 96.7% 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 11:07:27 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5402 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: 2.195002 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 2.195002 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 856.7913 centred at (gu) : 86.93952 91.99957 82.15433 assigned negative charge : -844.8000 centred at (gu) : 86.82658 92.22563 82.04619 start vw surface at 0.2400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 218754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44171 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 97028 mr = 162687 m= 22385 mr = 76535 m= 2554 mr = 15890 m= 104 mr = 1466 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 6578 time to turn everything in is 1.680000 number of dielectric boundary points 84228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 41765 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) : 1.463334 object centre at (A) : -11.71000 5.882999 41.22550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0498055E-02 5.5225484E-02 midg,1,midg; midg,igrid,midg 0.1641660 -0.8140524 1,midg,midg; igrid,midg,midg -2.9183038E-02 0.2656577 gauss-seidel spectral radius is 0.9991143 estimated iterations to convergence 265 setup time was (sec) 1.990000 now iterating at: 11:07:30 rms-change max change #iterations 10.38602 315.3583 at 10iterations 5.812890 148.7811 at 20iterations 3.232141 93.75600 at 30iterations 1.791585 48.07496 at 40iterations 0.9879515 22.52338 at 50iterations 0.5439690 10.98074 at 60iterations 0.2987039 6.313857 at 70iterations 0.1638093 3.231544 at 80iterations 8.9650065E-02 1.797831 at 90iterations 4.9082182E-02 0.9311886 at 100iterations 2.6887678E-02 0.4870634 at 110iterations 1.4701812E-02 0.2639856 at 120iterations 8.0324402E-03 0.1450691 at 130iterations 4.4029537E-03 8.1752777E-02 at 140iterations 2.4102970E-03 4.9704552E-02 at 150iterations 1.3377750E-03 2.4717331E-02 at 160iterations 7.5360533E-04 1.4493942E-02 at 170iterations 4.3997780E-04 9.1667175E-03 at 180iterations finished qdiffx linear iterations at : 11:07:40 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 4.3997780E-04 9.1667175E-03 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 11:07:41 12.757u 0.184s 0:13.21 97.8% 0+0k 0+0io 0pf+0w