Mon Oct 10 10:22:40 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 10:22:40 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 = 2762 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5881478 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): -20.15800 40.37100 ymin,ymax (A): -11.29400 43.83200 zmin,zma (A): -1.385000 53.55400 x,y,z range (A): 60.52900 55.12600 54.93900 scale (grids/A): 0.5881478 object centre (A): 10.10650 16.26900 26.08450 number of atom coordinates read : 2762 total number of charged atoms : 2617 net assigned charge : 13.00002 assigned positive charge : 404.8421 centred at (gu) : 91.75870 91.19695 86.28992 assigned negative charge : -391.8425 centred at (gu) : 91.90327 91.25504 86.03765 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6554 nv = 96 ne = 84 npr = 52784 no. pairs analyzed = 52784 no. exposed pairs = 4132 no. arc points = 29752 no. surface atoms = 1367 nbur = 1395 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= 324 mr = 2950 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2945 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8092 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2228231E-09 4.3624540E-09 midg,1,midg; midg,igrid,midg 4.1671253E-09 3.3750926E-09 1,midg,midg; igrid,midg,midg 5.0598108E-09 5.0354160E-10 gauss-seidel spectral radius is 0.9850772 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 10:22:41 rms-change max change #iterations 9.8829105E-02 16.10966 at 10iterations 7.8444956E-03 1.270973 at 20iterations 6.4951571E-04 0.1240730 at 30iterations 6.5468099E-05 8.4686279E-03 at 40iterations 1.0378104E-05 1.0740757E-03 at 50iterations finished qdiffx linear iterations at : 10:22:44 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.0378104E-05 1.0740757E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 10:22:44 3.425u 0.190s 0:03.98 90.7% 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 10:22:44 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 = 2762 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.764444 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): -20.15800 40.37100 ymin,ymax (A): -11.29400 43.83200 zmin,zma (A): -1.385000 53.55400 x,y,z range (A): 60.52900 55.12600 54.93900 scale (grids/A): 1.764444 object centre (A): 10.10650 16.26900 26.08450 number of atom coordinates read : 2762 total number of charged atoms : 2617 net assigned charge : 13.00002 assigned positive charge : 404.8421 centred at (gu) : 95.27560 93.59058 78.86911 assigned negative charge : -391.8425 centred at (gu) : 95.70966 93.76484 78.11266 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29752 grid for indexing accessible points = 1.400000 m= 23004 mr = 43402 m= 3036 mr = 15026 m= 106 mr = 1483 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 36332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20346 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) : 0.5881478 object centre at (A) : 10.10650 16.26900 26.08450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8560498E-04 1.9909719E-02 midg,1,midg; midg,igrid,midg 2.3493102E-02 2.8935848E-02 1,midg,midg; igrid,midg,midg 1.6012534E-02 1.8022519E-02 gauss-seidel spectral radius is 0.9984421 estimated iterations to convergence 201 setup time was (sec) 0.5800000 now iterating at: 10:22:45 rms-change max change #iterations 3.676636 141.2272 at 10iterations 1.621201 62.39903 at 20iterations 0.7169127 24.02629 at 30iterations 0.3174132 10.55809 at 40iterations 0.1411048 4.717339 at 50iterations 6.2188182E-02 2.159754 at 60iterations 2.7535645E-02 1.041702 at 70iterations 1.2237563E-02 0.4296513 at 80iterations 5.4156901E-03 0.1827154 at 90iterations 2.4067515E-03 7.8990936E-02 at 100iterations 1.0710954E-03 3.7063599E-02 at 110iterations 4.7687485E-04 1.7829895E-02 at 120iterations finished qdiffx linear iterations at : 10:22:52 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 4.7687485E-04 1.7829895E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 10:22:53 7.888u 0.212s 0:08.46 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 Mon Oct 10 2011 at 10:22:53 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 = 2762 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.646665 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): -20.15800 40.37100 ymin,ymax (A): -11.29400 43.83200 zmin,zma (A): -1.385000 53.55400 x,y,z range (A): 60.52900 55.12600 54.93900 scale (grids/A): 2.646665 object centre (A): 10.10650 16.26900 26.08450 number of atom coordinates read : 2762 total number of charged atoms : 2617 net assigned charge : 13.00002 assigned positive charge : 404.8421 centred at (gu) : 97.91335 95.38583 73.30360 assigned negative charge : -391.8425 centred at (gu) : 98.56438 95.64733 72.16902 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29752 grid for indexing accessible points = 1.400000 m= 74771 mr = 107312 m= 25040 mr = 56583 m= 4875 mr = 18216 m= 475 mr = 3129 m= 14 mr = 219 m= 0 mr = 2 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 82070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 20932 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) : 1.764444 object centre at (A) : 10.10650 16.26900 26.08450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5998274E-02 0.2118890 midg,1,midg; midg,igrid,midg 0.3722014 0.3206428 1,midg,midg; igrid,midg,midg 0.2710193 0.2899367 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 1.120000 now iterating at: 10:22:54 rms-change max change #iterations 9.436352 279.4049 at 10iterations 5.601855 191.6002 at 20iterations 3.276960 81.33994 at 30iterations 1.896960 49.37598 at 40iterations 1.096252 29.59894 at 50iterations 0.6303969 16.22329 at 60iterations 0.3608148 8.432334 at 70iterations 0.2065576 4.618027 at 80iterations 0.1176721 2.867104 at 90iterations 6.7144871E-02 1.376070 at 100iterations 3.8234834E-02 0.8308220 at 110iterations 2.1696147E-02 0.4748421 at 120iterations 1.2351318E-02 0.2509718 at 130iterations 7.0088929E-03 0.1440201 at 140iterations 3.9769756E-03 8.2028151E-02 at 150iterations 2.2574966E-03 5.1210403E-02 at 160iterations 1.2803380E-03 2.5849342E-02 at 170iterations 7.2838581E-04 1.4844894E-02 at 180iterations finished qdiffx linear iterations at : 10:23:05 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 7.2838581E-04 1.4844894E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 10:23:06 12.688u 0.205s 0:13.17 97.7% 0+0k 0+0io 0pf+0w