Sat Oct 15 14:32:58 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 14:32:59 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4150 !!! WARNING: HIT 104 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5329980 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): -2.194000 57.08400 ymin,ymax (A): -5.982000 59.89600 zmin,zma (A): 29.24500 96.03699 x,y,z range (A): 59.27800 65.87800 66.79199 scale (grids/A): 0.5329980 object centre (A): 27.44500 26.95700 62.64100 number of atom coordinates read : 4150 total number of charged atoms : 3999 net assigned charge : -3.985965 assigned positive charge : 641.7137 centred at (gu) : 89.85718 88.75988 90.10574 assigned negative charge : -645.7036 centred at (gu) : 89.96556 88.78888 90.08040 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7761 nv = 96 ne = 84 npr = 78798 no. pairs analyzed = 78798 no. exposed pairs = 6040 no. arc points = 42773 no. surface atoms = 1972 nbur = 2178 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 = 1.596000 m= 304 mr = 3569 m= 4 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 4493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4194 ## 548 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 10228 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9179426E-10 -2.3992715E-12 midg,1,midg; midg,igrid,midg 2.8936232E-11 -2.3558383E-10 1,midg,midg; igrid,midg,midg 4.9427040E-10 -7.6665618E-10 gauss-seidel spectral radius is 0.9819660 estimated iterations to convergence 61 setup time was (sec) 0.4700000 now iterating at: 14:32:59 rms-change max change #iterations 7.7845983E-02 11.40093 at 10iterations 5.0647473E-03 0.8867788 at 20iterations 5.5927353E-04 7.2814941E-02 at 30iterations 1.4669291E-04 1.2623310E-02 at 40iterations 4.4938508E-05 3.7808418E-03 at 50iterations finished qdiffx linear iterations at : 14:33:05 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 4.4938508E-05 3.7808418E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 14:33:05 3.584u 0.197s 0:06.72 56.1% 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 14:33:05 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4150 !!! WARNING: HIT 104 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.598994 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): -2.194000 57.08400 ymin,ymax (A): -5.982000 59.89600 zmin,zma (A): 29.24500 96.03699 x,y,z range (A): 59.27800 65.87800 66.79199 scale (grids/A): 1.598994 object centre (A): 27.44500 26.95700 62.64100 number of atom coordinates read : 4150 total number of charged atoms : 3999 net assigned charge : -3.985965 assigned positive charge : 641.7137 centred at (gu) : 89.57000 86.27829 90.31551 assigned negative charge : -645.7036 centred at (gu) : 89.89642 86.36642 90.24062 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 85442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42773 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25775 mr = 54533 m= 2503 mr = 16334 m= 68 mr = 956 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 713 time to turn everything in is 0.4400000 number of dielectric boundary points 41965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 446 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 30446 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) : 0.5329980 object centre at (A) : 27.44500 26.95700 62.64100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1299705E-04 -1.2671948E-02 midg,1,midg; midg,igrid,midg 1.6166916E-03 -3.3389325E-03 1,midg,midg; igrid,midg,midg -3.7333096E-04 -9.3356343E-03 gauss-seidel spectral radius is 0.9982558 estimated iterations to convergence 190 setup time was (sec) 0.6700000 now iterating at: 14:33:06 rms-change max change #iterations 3.943855 172.4236 at 10iterations 1.664682 60.78767 at 20iterations 0.7008868 22.37307 at 30iterations 0.2966669 10.15874 at 40iterations 0.1254761 4.374628 at 50iterations 5.3157929E-02 1.646554 at 60iterations 2.2597948E-02 0.8384857 at 70iterations 9.5519777E-03 0.3130302 at 80iterations 4.0919930E-03 0.1386546 at 90iterations 1.7464559E-03 5.9335709E-02 at 100iterations 7.5848546E-04 2.3223877E-02 at 110iterations 3.3829370E-04 1.1459351E-02 at 120iterations finished qdiffx linear iterations at : 14:33:18 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 3.3829370E-04 1.1459351E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 14:33:19 8.454u 0.227s 0:13.55 63.9% 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 Sat Oct 15 2011 at 14:33:19 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4150 !!! WARNING: HIT 104 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.398491 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): -2.194000 57.08400 ymin,ymax (A): -5.982000 59.89600 zmin,zma (A): 29.24500 96.03699 x,y,z range (A): 59.27800 65.87800 66.79199 scale (grids/A): 2.398491 object centre (A): 27.44500 26.95700 62.64100 number of atom coordinates read : 4150 total number of charged atoms : 3999 net assigned charge : -3.985965 assigned positive charge : 641.7137 centred at (gu) : 89.35446 84.41698 90.47295 assigned negative charge : -645.7036 centred at (gu) : 89.84461 84.54939 90.36086 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 198596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42773 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 88477 mr = 135059 m= 24670 mr = 66576 m= 3683 mr = 17264 m= 252 mr = 2041 m= 5 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 2189 time to turn everything in is 1.050000 number of dielectric boundary points 94671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 31949 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) : 1.598994 object centre at (A) : 27.44500 26.95700 62.64100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9237129E-02 -0.1874451 midg,1,midg; midg,igrid,midg 0.2239747 1.5094539E-02 1,midg,midg; igrid,midg,midg -1.7692270E-02 -4.0710419E-02 gauss-seidel spectral radius is 0.9992096 estimated iterations to convergence 281 setup time was (sec) 1.330000 now iterating at: 14:33:21 rms-change max change #iterations 10.58213 281.7473 at 10iterations 6.194074 152.8005 at 20iterations 3.601697 85.03098 at 30iterations 2.077230 42.36373 at 40iterations 1.192688 26.48385 at 50iterations 0.6837161 14.87603 at 60iterations 0.3906777 8.282663 at 70iterations 0.2221357 4.686867 at 80iterations 0.1265129 2.582338 at 90iterations 7.1789160E-02 1.386908 at 100iterations 4.0745560E-02 0.8395405 at 110iterations 2.3081731E-02 0.5173006 at 120iterations 1.3071970E-02 0.2719016 at 130iterations 7.3980647E-03 0.1437378 at 140iterations 4.1765971E-03 7.6322556E-02 at 150iterations 2.3653670E-03 4.4715881E-02 at 160iterations 1.3372821E-03 2.6926041E-02 at 170iterations 7.5455004E-04 1.3673306E-02 at 180iterations finished qdiffx linear iterations at : 14:33:48 total time elapsed so far: 14.60000 # loops : 180 mean,max change (kT/e) : 7.5455004E-04 1.3673306E-02 energy calculations done at 14.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.73000 DelPhi exited at 14:33:49 14.732u 0.278s 0:29.48 50.8% 0+0k 0+0io 0pf+0w