Mon Oct 10 19:43:28 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 Mon Oct 10 2011 at 19:43:28 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3726 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: 0.5420549 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): 7.2000027E-02 65.74800 ymin,ymax (A): -8.736000 38.58000 zmin,zma (A): -19.82600 41.12500 x,y,z range (A): 65.67600 47.31600 60.95100 scale (grids/A): 0.5420549 object centre (A): 32.91000 14.92200 10.64950 number of atom coordinates read : 3726 total number of charged atoms : 3563 net assigned charge : -11.99995 assigned positive charge : 552.2249 centred at (gu) : 88.81573 89.66994 90.73784 assigned negative charge : -564.2267 centred at (gu) : 88.82213 89.72822 90.83711 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6984 nv = 96 ne = 84 npr = 77522 no. pairs analyzed = 77522 no. exposed pairs = 4488 no. arc points = 30107 no. surface atoms = 1522 nbur = 2204 mkacc time = 0.1300000 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 = 1.568000 m= 301 mr = 3811 m= 0 mr = 20 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3027 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9237 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9550524E-11 -1.6399601E-09 midg,1,midg; midg,igrid,midg -2.3063347E-10 -9.7815700E-10 1,midg,midg; igrid,midg,midg -7.8383988E-10 -5.1206489E-10 gauss-seidel spectral radius is 0.9825075 estimated iterations to convergence 62 setup time was (sec) 0.4500000 now iterating at: 19:43:29 rms-change max change #iterations 8.2743116E-02 12.62262 at 10iterations 7.2259414E-03 1.401543 at 20iterations 1.2474009E-03 0.1460876 at 30iterations 3.3850555E-04 4.6314240E-02 at 40iterations 9.9414639E-05 1.4433861E-02 at 50iterations finished qdiffx linear iterations at : 19:43:32 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 9.9414639E-05 1.4433861E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 19:43:33 3.527u 0.175s 0:04.05 91.1% 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 Mon Oct 10 2011 at 19:43:33 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3726 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: 1.626165 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): 7.2000027E-02 65.74800 ymin,ymax (A): -8.736000 38.58000 zmin,zma (A): -19.82600 41.12500 x,y,z range (A): 65.67600 47.31600 60.95100 scale (grids/A): 1.626165 object centre (A): 32.91000 14.92200 10.64950 number of atom coordinates read : 3726 total number of charged atoms : 3563 net assigned charge : -11.99995 assigned positive charge : 552.2249 centred at (gu) : 86.44629 89.00900 92.21244 assigned negative charge : -564.2267 centred at (gu) : 86.46605 89.18427 92.51104 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 78693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30107 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25210 mr = 55719 m= 2689 mr = 17697 m= 84 mr = 1359 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.4000000 number of dielectric boundary points 31898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 27275 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) : 0.5420549 object centre at (A) : 32.91000 14.92200 10.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4181232E-03 -2.8548352E-02 midg,1,midg; midg,igrid,midg -1.0969331E-02 -1.3210364E-02 1,midg,midg; igrid,midg,midg -5.4960987E-03 -7.9323845E-03 gauss-seidel spectral radius is 0.9982388 estimated iterations to convergence 189 setup time was (sec) 0.6200000 now iterating at: 19:43:33 rms-change max change #iterations 3.730893 155.2125 at 10iterations 1.580852 57.63620 at 20iterations 0.6699430 22.74506 at 30iterations 0.2848372 10.36225 at 40iterations 0.1205070 4.031380 at 50iterations 5.1329114E-02 1.727013 at 60iterations 2.1872230E-02 0.7561684 at 70iterations 9.4734160E-03 0.3250222 at 80iterations 4.1608778E-03 0.1248932 at 90iterations 1.9159862E-03 6.4943314E-02 at 100iterations 9.4923482E-04 3.2886505E-02 at 110iterations 5.1531091E-04 1.6543865E-02 at 120iterations finished qdiffx linear iterations at : 19:43:41 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 5.1531091E-04 1.6543865E-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 19:43:41 7.936u 0.207s 0:08.57 94.8% 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 19:43:41 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3726 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: 2.439247 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): 7.2000027E-02 65.74800 ymin,ymax (A): -8.736000 38.58000 zmin,zma (A): -19.82600 41.12500 x,y,z range (A): 65.67600 47.31600 60.95100 scale (grids/A): 2.439247 object centre (A): 32.91000 14.92200 10.64950 number of atom coordinates read : 3726 total number of charged atoms : 3563 net assigned charge : -11.99995 assigned positive charge : 552.2249 centred at (gu) : 84.66888 88.51308 93.31818 assigned negative charge : -564.2267 centred at (gu) : 84.69902 88.77631 93.76630 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 183206 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30107 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 87545 mr = 136294 m= 25128 mr = 70262 m= 4355 mr = 18950 m= 328 mr = 2822 m= 2 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 800 time to turn everything in is 0.9600000 number of dielectric boundary points 72080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 28464 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) : 1.626165 object centre at (A) : 32.91000 14.92200 10.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3866706 -0.4543959 midg,1,midg; midg,igrid,midg -0.1779797 -0.1796869 1,midg,midg; igrid,midg,midg 2.0109233E-02 -0.3960963 gauss-seidel spectral radius is 0.9991671 estimated iterations to convergence 274 setup time was (sec) 1.200000 now iterating at: 19:43:43 rms-change max change #iterations 9.703807 295.0385 at 10iterations 5.509571 135.1116 at 20iterations 3.116245 65.65370 at 30iterations 1.750855 38.02282 at 40iterations 0.9836977 21.01680 at 50iterations 0.5501549 10.20554 at 60iterations 0.3080555 5.811783 at 70iterations 0.1720419 3.150423 at 80iterations 9.6080780E-02 1.910378 at 90iterations 5.3734291E-02 1.133797 at 100iterations 3.0019054E-02 0.5724530 at 110iterations 1.6866414E-02 0.3199596 at 120iterations 9.5067406E-03 0.1816139 at 130iterations 5.4242671E-03 0.1037302 at 140iterations 3.1521770E-03 5.7641983E-02 at 150iterations 1.8915480E-03 3.7563324E-02 at 160iterations 1.1821707E-03 2.2621155E-02 at 170iterations 7.7518361E-04 1.5182495E-02 at 180iterations finished qdiffx linear iterations at : 19:43:54 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 7.7518361E-04 1.5182495E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 19:43:54 12.666u 0.218s 0:13.19 97.5% 0+0k 0+0io 0pf+0w