Sat Oct 15 12:02:09 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 Sat Oct 15 2011 at 12:02:09 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: HIT 84 has a net charge of 0.5140 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 : 12.51402 assigned positive charge : 376.9959 centred at (gu) : 89.86311 90.07856 90.63438 assigned negative charge : -364.4828 centred at (gu) : 89.83879 90.06583 90.58687 start vw surface at 9.0000004E-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 = 8.0000006E-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 = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2000000 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 0.2700000 number of grid points assigned charge 7482 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3499083E-09 5.9044765E-09 midg,1,midg; midg,igrid,midg 3.5255527E-09 4.3106350E-09 1,midg,midg; igrid,midg,midg 3.3925334E-09 4.3919908E-09 gauss-seidel spectral radius is 0.9851675 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 12:02:10 rms-change max change #iterations 9.7792536E-02 14.66716 at 10iterations 8.1480835E-03 1.283749 at 20iterations 9.1368897E-04 0.1493511 at 30iterations 2.3049899E-04 4.6630859E-02 at 40iterations 7.8041681E-05 1.6392708E-02 at 50iterations finished qdiffx linear iterations at : 12:02:13 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.8041681E-05 1.6392708E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 12:02:13 3.447u 0.219s 0:03.99 91.4% 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 Sat Oct 15 2011 at 12:02:13 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: HIT 84 has a net charge of 0.5140 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 : 12.51402 assigned positive charge : 376.9959 centred at (gu) : 89.58887 90.23499 91.90263 assigned negative charge : -364.4828 centred at (gu) : 89.51641 90.19748 91.76036 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 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 = 0.1500000 no. cavity mid-points inaccessible to solvent = 1298 time to turn everything in is 0.3100000 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 0.4000000 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 3.0773615E-03 2.0418391E-02 midg,1,midg; midg,igrid,midg 3.3239339E-02 1.4556448E-02 1,midg,midg; igrid,midg,midg 2.7362788E-02 2.8834041E-02 gauss-seidel spectral radius is 0.9984335 estimated iterations to convergence 200 setup time was (sec) 0.5500000 now iterating at: 12:02:14 rms-change max change #iterations 3.629049 155.3080 at 10iterations 1.598808 56.55774 at 20iterations 0.7068405 26.75863 at 30iterations 0.3127572 11.71759 at 40iterations 0.1389171 5.147799 at 50iterations 6.1563324E-02 2.258331 at 60iterations 2.7471995E-02 0.8891649 at 70iterations 1.2245441E-02 0.4301243 at 80iterations 5.5178157E-03 0.1922884 at 90iterations 2.5201950E-03 0.1006317 at 100iterations 1.2154564E-03 4.5642853E-02 at 110iterations 6.2309322E-04 2.8026581E-02 at 120iterations finished qdiffx linear iterations at : 12:02:21 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 6.2309322E-04 2.8026581E-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 12:02:22 7.935u 0.218s 0:08.51 95.6% 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 12:02:22 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: HIT 84 has a net charge of 0.5140 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 : 12.51402 assigned positive charge : 376.9959 centred at (gu) : 89.38315 90.35232 92.85375 assigned negative charge : -364.4828 centred at (gu) : 89.27454 90.29613 92.64049 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 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 = 0.4600000 no. cavity mid-points inaccessible to solvent = 4359 time to turn everything in is 0.8200000 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 0.9200000 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 1.6736144E-02 0.2555723 midg,1,midg; midg,igrid,midg 0.5609115 0.2606035 1,midg,midg; igrid,midg,midg 0.3086614 0.3481379 gauss-seidel spectral radius is 0.9992075 estimated iterations to convergence 280 setup time was (sec) 1.070000 now iterating at: 12:02:23 rms-change max change #iterations 8.991641 374.3521 at 10iterations 5.233487 154.3629 at 20iterations 3.008980 72.41394 at 30iterations 1.723819 41.14074 at 40iterations 0.9847214 23.55496 at 50iterations 0.5622361 12.72962 at 60iterations 0.3196859 7.068234 at 70iterations 0.1810782 3.988733 at 80iterations 0.1028210 2.011703 at 90iterations 5.8252420E-02 1.441185 at 100iterations 3.2914426E-02 0.6778717 at 110iterations 1.8643809E-02 0.3839569 at 120iterations 1.0535633E-02 0.2417173 at 130iterations 5.9851343E-03 0.1182199 at 140iterations 3.3968936E-03 7.2029114E-02 at 150iterations 1.9482201E-03 3.9161682E-02 at 160iterations 1.1383210E-03 2.9632568E-02 at 170iterations 6.8512897E-04 1.5510559E-02 at 180iterations finished qdiffx linear iterations at : 12:02:35 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 6.8512897E-04 1.5510559E-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) 12.81000 DelPhi exited at 12:02:35 12.817u 0.269s 0:13.61 96.0% 0+0k 0+0io 0pf+0w