Tue Oct 11 04:29:35 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 Tue Oct 11 2011 at 04:29:35 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6648985 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): -12.58100 37.07800 ymin,ymax (A): -25.99200 22.47600 zmin,zma (A): -8.297000 45.24500 x,y,z range (A): 49.65900 48.46800 53.54200 scale (grids/A): 0.6648985 object centre (A): 12.24850 -1.757999 18.47400 number of atom coordinates read : 2750 total number of charged atoms : 2597 net assigned charge : 1.140015 assigned positive charge : 414.2667 centred at (gu) : 90.45960 90.37822 91.21835 assigned negative charge : -413.1273 centred at (gu) : 90.22693 90.22857 91.12365 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8121 nv = 96 ne = 84 npr = 56846 no. pairs analyzed = 56846 no. exposed pairs = 3342 no. arc points = 23175 no. surface atoms = 1121 nbur = 1629 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4650 m= 8 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2100000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2245 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9618 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5557722E-08 3.2343582E-08 midg,1,midg; midg,igrid,midg -3.0985674E-08 4.0905213E-08 1,midg,midg; igrid,midg,midg -4.9156760E-08 6.2556261E-08 gauss-seidel spectral radius is 0.9882842 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 04:29:36 rms-change max change #iterations 0.1805487 25.33530 at 10iterations 1.9763222E-02 2.490019 at 20iterations 2.1687630E-03 0.2884979 at 30iterations 2.5042368E-04 3.0738831E-02 at 40iterations 3.3102198E-05 4.4126511E-03 at 50iterations finished qdiffx linear iterations at : 04:29:39 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.3102198E-05 4.4126511E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 04:29:39 3.376u 0.187s 0:04.13 85.9% 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 Tue Oct 11 2011 at 04:29:39 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.994696 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): -12.58100 37.07800 ymin,ymax (A): -25.99200 22.47600 zmin,zma (A): -8.297000 45.24500 x,y,z range (A): 49.65900 48.46800 53.54200 scale (grids/A): 1.994696 object centre (A): 12.24850 -1.757999 18.47400 number of atom coordinates read : 2750 total number of charged atoms : 2597 net assigned charge : 1.140015 assigned positive charge : 414.2667 centred at (gu) : 91.37808 91.13400 93.65425 assigned negative charge : -413.1273 centred at (gu) : 90.68076 90.68542 93.37070 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 87102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23175 grid for indexing accessible points = 1.400000 m= 32801 mr = 61936 m= 5321 mr = 24532 m= 331 mr = 3272 m= 4 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 349 time to turn everything in is 0.4100000 number of dielectric boundary points 35698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20530 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) : 0.6648985 object centre at (A) : 12.24850 -1.757999 18.47400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2903710E-02 -1.3836744E-03 midg,1,midg; midg,igrid,midg -1.6064232E-02 1.9419137E-02 1,midg,midg; igrid,midg,midg -5.4095713E-03 8.3671913E-02 gauss-seidel spectral radius is 0.9987632 estimated iterations to convergence 225 setup time was (sec) 0.6100000 now iterating at: 04:29:40 rms-change max change #iterations 4.819272 179.9528 at 10iterations 2.346068 74.24028 at 20iterations 1.144813 35.62910 at 30iterations 0.5557156 15.85929 at 40iterations 0.2710748 7.582943 at 50iterations 0.1313240 3.857203 at 60iterations 6.4230345E-02 1.952683 at 70iterations 3.1202987E-02 0.9231014 at 80iterations 1.5210046E-02 0.4363785 at 90iterations 7.3885932E-03 0.2150326 at 100iterations 3.6102063E-03 0.1006663 at 110iterations 1.7668597E-03 5.0079346E-02 at 120iterations finished qdiffx linear iterations at : 04:29:47 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 1.7668597E-03 5.0079346E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 04:29:48 7.842u 0.222s 0:08.55 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 Tue Oct 11 2011 at 04:29:48 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.992043 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): -12.58100 37.07800 ymin,ymax (A): -25.99200 22.47600 zmin,zma (A): -8.297000 45.24500 x,y,z range (A): 49.65900 48.46800 53.54200 scale (grids/A): 2.992043 object centre (A): 12.24850 -1.757999 18.47400 number of atom coordinates read : 2750 total number of charged atoms : 2597 net assigned charge : 1.140015 assigned positive charge : 414.2667 centred at (gu) : 92.06711 91.70083 95.48146 assigned negative charge : -413.1273 centred at (gu) : 91.02100 91.02808 95.05596 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 201518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23175 grid for indexing accessible points = 1.400000 m= 105527 mr = 149761 m= 38999 mr = 87194 m= 9503 mr = 31569 m= 1442 mr = 7015 m= 119 mr = 962 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1288 time to turn everything in is 1.150000 number of dielectric boundary points 80554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 20768 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) : 1.994696 object centre at (A) : 12.24850 -1.757999 18.47400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7302728 0.2135261 midg,1,midg; midg,igrid,midg -0.1572606 0.2278799 1,midg,midg; igrid,midg,midg -2.2686470E-02 0.7379619 gauss-seidel spectral radius is 0.9992908 estimated iterations to convergence 296 setup time was (sec) 1.400000 now iterating at: 04:29:50 rms-change max change #iterations 11.05144 440.5421 at 10iterations 6.513920 139.8960 at 20iterations 3.837178 79.40947 at 30iterations 2.253274 46.87579 at 40iterations 1.323031 24.99159 at 50iterations 0.7747293 14.26244 at 60iterations 0.4525684 7.443150 at 70iterations 0.2647861 4.911090 at 80iterations 0.1547779 2.608445 at 90iterations 9.0346374E-02 1.534550 at 100iterations 5.2782387E-02 0.9451027 at 110iterations 3.0819146E-02 0.5188637 at 120iterations 1.7944390E-02 0.2914658 at 130iterations 1.0514721E-02 0.1839180 at 140iterations 6.1378470E-03 0.1123772 at 150iterations 3.6009955E-03 6.1336517E-02 at 160iterations 2.1332989E-03 3.9966583E-02 at 170iterations 1.2714210E-03 2.1842957E-02 at 180iterations finished qdiffx linear iterations at : 04:30:01 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.2714210E-03 2.1842957E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 04:30:02 12.970u 0.206s 0:13.78 95.5% 0+0k 0+0io 0pf+0w