Sat Oct 15 12:01:43 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 Sat Oct 15 2011 at 12:01:43 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 = 2564 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5905283 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): -14.83800 41.20900 ymin,ymax (A): -30.71600 29.56900 zmin,zma (A): -9.654000 32.47000 x,y,z range (A): 56.04700 60.28500 42.12400 scale (grids/A): 0.5905283 object centre (A): 13.18550 -0.5734997 11.40800 number of atom coordinates read : 2564 total number of charged atoms : 2428 net assigned charge : 12.50002 assigned positive charge : 372.9539 centred at (gu) : 89.88268 90.14275 90.64395 assigned negative charge : -360.4548 centred at (gu) : 89.86357 90.13166 90.60052 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6024 nv = 96 ne = 84 npr = 51056 no. pairs analyzed = 51056 no. exposed pairs = 3403 no. arc points = 24212 no. surface atoms = 1137 nbur = 1427 mkacc time = 9.0000004E-02 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 = 1.456000 m= 304 mr = 3063 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.1900000 number of dielectric boundary points 3245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2412 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7482 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4422702E-09 5.7782774E-09 midg,1,midg; midg,igrid,midg 3.5152989E-09 4.3220370E-09 1,midg,midg; igrid,midg,midg 3.5159786E-09 4.2734767E-09 gauss-seidel spectral radius is 0.9851675 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 12:01:43 rms-change max change #iterations 9.4711713E-02 15.27678 at 10iterations 7.8621730E-03 1.320229 at 20iterations 8.5889595E-04 0.1408463 at 30iterations 2.1280033E-04 4.2654991E-02 at 40iterations 7.1678951E-05 1.5021324E-02 at 50iterations finished qdiffx linear iterations at : 12:01:46 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 7.1678951E-05 1.5021324E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 12:01:47 3.452u 0.220s 0:04.07 90.1% 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 Sat Oct 15 2011 at 12:01:47 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 = 2564 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.771585 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): -14.83800 41.20900 ymin,ymax (A): -30.71600 29.56900 zmin,zma (A): -9.654000 32.47000 x,y,z range (A): 56.04700 60.28500 42.12400 scale (grids/A): 1.771585 object centre (A): 13.18550 -0.5734997 11.40800 number of atom coordinates read : 2564 total number of charged atoms : 2428 net assigned charge : 12.50002 assigned positive charge : 372.9539 centred at (gu) : 89.64760 90.42753 91.93134 assigned negative charge : -360.4548 centred at (gu) : 89.59081 90.39500 91.80133 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24212 grid for indexing accessible points = 1.400000 m= 21742 mr = 43712 m= 3064 mr = 15031 m= 188 mr = 1724 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1298 time to turn everything in is 0.3300000 number of dielectric boundary points 29878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 18913 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) : 0.5905283 object centre at (A) : 13.18550 -0.5734997 11.40800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2600879E-03 1.9880267E-02 midg,1,midg; midg,igrid,midg 3.3335440E-02 1.4443317E-02 1,midg,midg; igrid,midg,midg 2.7928809E-02 2.8819788E-02 gauss-seidel spectral radius is 0.9984335 estimated iterations to convergence 200 setup time was (sec) 0.5500000 now iterating at: 12:01:48 rms-change max change #iterations 3.575063 155.3080 at 10iterations 1.574530 56.55770 at 20iterations 0.6961161 27.44941 at 30iterations 0.3079429 11.40499 at 40iterations 0.1367823 5.074359 at 50iterations 6.0650729E-02 2.147480 at 60iterations 2.7060160E-02 0.9069309 at 70iterations 1.2047619E-02 0.4235764 at 80iterations 5.4157530E-03 0.2003684 at 90iterations 2.4688365E-03 9.5748901E-02 at 100iterations 1.1808202E-03 4.2800903E-02 at 110iterations 5.9833215E-04 2.5964737E-02 at 120iterations finished qdiffx linear iterations at : 12:01:55 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 5.9833215E-04 2.5964737E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 12:01:55 7.931u 0.215s 0:08.50 95.7% 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 Sat Oct 15 2011 at 12:01:55 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 = 2564 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.657377 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): -14.83800 41.20900 ymin,ymax (A): -30.71600 29.56900 zmin,zma (A): -9.654000 32.47000 x,y,z range (A): 56.04700 60.28500 42.12400 scale (grids/A): 2.657377 object centre (A): 13.18550 -0.5734997 11.40800 number of atom coordinates read : 2564 total number of charged atoms : 2428 net assigned charge : 12.50002 assigned positive charge : 372.9539 centred at (gu) : 89.47131 90.64109 92.89684 assigned negative charge : -360.4548 centred at (gu) : 89.38611 90.59241 92.70197 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 151595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24212 grid for indexing accessible points = 1.400000 m= 71876 mr = 106760 m= 24155 mr = 56740 m= 5465 mr = 18580 m= 759 mr = 3822 m= 42 mr = 442 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 4359 time to turn everything in is 0.8100000 number of dielectric boundary points 67532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 19420 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) : 1.771585 object centre at (A) : 13.18550 -0.5734997 11.40800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8773295E-02 0.2494407 midg,1,midg; midg,igrid,midg 0.5644135 0.2591783 1,midg,midg; igrid,midg,midg 0.3170612 0.3486480 gauss-seidel spectral radius is 0.9992075 estimated iterations to convergence 280 setup time was (sec) 1.060000 now iterating at: 12:01:57 rms-change max change #iterations 8.871915 374.3521 at 10iterations 5.167393 154.4688 at 20iterations 2.972699 72.71754 at 30iterations 1.703854 41.71344 at 40iterations 0.9740984 23.02888 at 50iterations 0.5560878 12.94068 at 60iterations 0.3163398 6.890452 at 70iterations 0.1792559 3.953465 at 80iterations 0.1017595 2.003775 at 90iterations 5.7674725E-02 1.435898 at 100iterations 3.2595631E-02 0.6948700 at 110iterations 1.8465690E-02 0.3854485 at 120iterations 1.0430235E-02 0.2383718 at 130iterations 5.9206900E-03 0.1133273 at 140iterations 3.3565476E-03 6.9465637E-02 at 150iterations 1.9206231E-03 3.9093018E-02 at 160iterations 1.1167915E-03 2.9434204E-02 at 170iterations 6.6653726E-04 1.4999390E-02 at 180iterations finished qdiffx linear iterations at : 12:02:08 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 6.6653726E-04 1.4999390E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 12:02:09 12.769u 0.299s 0:13.51 96.5% 0+0k 0+0io 0pf+0w