Mon Oct 10 10:17:59 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 Mon Oct 10 2011 at 10:17:59 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2891 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5475323 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): -21.51400 43.50500 ymin,ymax (A): -12.54200 46.38300 zmin,zma (A): -1.750000 50.27800 x,y,z range (A): 65.01900 58.92500 52.02800 scale (grids/A): 0.5475323 object centre (A): 10.99550 16.92050 24.26400 number of atom coordinates read : 2891 total number of charged atoms : 2738 net assigned charge : 5.014015 assigned positive charge : 422.9778 centred at (gu) : 91.62114 91.77804 87.12028 assigned negative charge : -417.9643 centred at (gu) : 91.78037 91.82932 86.98544 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5801 nv = 96 ne = 84 npr = 55916 no. pairs analyzed = 55916 no. exposed pairs = 4405 no. arc points = 32247 no. surface atoms = 1446 nbur = 1445 mkacc time = 8.9999996E-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 = 1.568000 m= 254 mr = 2484 m= 0 mr = 8 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3187 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7571 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0847331E-09 6.1529432E-10 midg,1,midg; midg,igrid,midg 4.6190318E-10 6.2376250E-11 1,midg,midg; igrid,midg,midg 9.3551034E-10 -1.0237194E-09 gauss-seidel spectral radius is 0.9828122 estimated iterations to convergence 63 setup time was (sec) 0.3900000 now iterating at: 10:18:00 rms-change max change #iterations 7.1782954E-02 13.52368 at 10iterations 4.7206939E-03 0.8183036 at 20iterations 3.3365117E-04 5.6818008E-02 at 30iterations 3.1638458E-05 4.6119690E-03 at 40iterations 5.4048264E-06 5.4931641E-04 at 50iterations finished qdiffx linear iterations at : 10:18:02 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.4048264E-06 5.4931641E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 10:18:03 3.428u 0.180s 0:03.87 93.0% 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 10:18:03 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2891 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.642597 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): -21.51400 43.50500 ymin,ymax (A): -12.54200 46.38300 zmin,zma (A): -1.750000 50.27800 x,y,z range (A): 65.01900 58.92500 52.02800 scale (grids/A): 1.642597 object centre (A): 10.99550 16.92050 24.26400 number of atom coordinates read : 2891 total number of charged atoms : 2738 net assigned charge : 5.014015 assigned positive charge : 422.9778 centred at (gu) : 94.86318 95.33351 81.36031 assigned negative charge : -417.9643 centred at (gu) : 95.34084 95.48782 80.95599 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32247 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18881 mr = 37545 m= 2019 mr = 11791 m= 56 mr = 811 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.3300000 number of dielectric boundary points 33384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 352 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 21016 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) : 0.5475323 object centre at (A) : 10.99550 16.92050 24.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0280634E-03 4.5230412E-03 midg,1,midg; midg,igrid,midg 1.7394103E-02 3.6412014E-03 1,midg,midg; igrid,midg,midg 1.3378604E-02 -1.7425155E-02 gauss-seidel spectral radius is 0.9982154 estimated iterations to convergence 188 setup time was (sec) 0.5400000 now iterating at: 10:18:04 rms-change max change #iterations 3.236521 147.6284 at 10iterations 1.347898 60.00371 at 20iterations 0.5637673 24.23244 at 30iterations 0.2366529 8.342030 at 40iterations 9.8781295E-02 3.584880 at 50iterations 4.1254491E-02 1.561592 at 60iterations 1.7285865E-02 0.7224379 at 70iterations 7.2496780E-03 0.2715540 at 80iterations 3.0450625E-03 0.1137962 at 90iterations 1.2757381E-03 4.8633575E-02 at 100iterations 5.3409592E-04 2.3760796E-02 at 110iterations 2.2425577E-04 9.3326569E-03 at 120iterations finished qdiffx linear iterations at : 10:18:11 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.2425577E-04 9.3326569E-03 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 10:18:11 7.766u 0.206s 0:08.30 95.9% 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 Mon Oct 10 2011 at 10:18:11 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2891 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.463895 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): -21.51400 43.50500 ymin,ymax (A): -12.54200 46.38300 zmin,zma (A): -1.750000 50.27800 x,y,z range (A): 65.01900 58.92500 52.02800 scale (grids/A): 2.463895 object centre (A): 10.99550 16.92050 24.26400 number of atom coordinates read : 2891 total number of charged atoms : 2738 net assigned charge : 5.014015 assigned positive charge : 422.9778 centred at (gu) : 97.29446 97.99990 77.04030 assigned negative charge : -417.9643 centred at (gu) : 98.01109 98.23171 76.43392 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 145023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32247 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63404 mr = 93437 m= 18444 mr = 46586 m= 2827 mr = 12860 m= 169 mr = 1585 m= 1 mr = 48 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 466 time to turn everything in is 0.7900000 number of dielectric boundary points 75353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21877 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) : 1.642597 object centre at (A) : 10.99550 16.92050 24.26400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6149777E-02 4.9314525E-02 midg,1,midg; midg,igrid,midg 0.3999994 -9.3351252E-02 1,midg,midg; igrid,midg,midg 0.4893006 -0.5821562 gauss-seidel spectral radius is 0.9991571 estimated iterations to convergence 272 setup time was (sec) 1.030000 now iterating at: 10:18:12 rms-change max change #iterations 8.679434 403.0026 at 10iterations 5.007980 180.5385 at 20iterations 2.861966 85.36975 at 30iterations 1.617020 46.50796 at 40iterations 0.9122788 25.00847 at 50iterations 0.5100625 12.65569 at 60iterations 0.2859325 7.941833 at 70iterations 0.1591872 4.503305 at 80iterations 8.8868231E-02 2.287340 at 90iterations 4.9356420E-02 1.291525 at 100iterations 2.7423939E-02 0.5919285 at 110iterations 1.5214001E-02 0.3226452 at 120iterations 8.4284479E-03 0.2039185 at 130iterations 4.6704812E-03 0.1054873 at 140iterations 2.5841631E-03 5.6978226E-02 at 150iterations 1.4331264E-03 3.1028748E-02 at 160iterations 7.9288136E-04 2.0098686E-02 at 170iterations 4.3857296E-04 1.0906219E-02 at 180iterations finished qdiffx linear iterations at : 10:18:24 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 4.3857296E-04 1.0906219E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 10:18:24 12.471u 0.207s 0:12.97 97.6% 0+0k 0+0io 0pf+0w