Sun Oct 9 07:05:12 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 Sun Oct 9 2011 at 07:05:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.6759835 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): -40.92800 1.897000 ymin,ymax (A): -32.29900 12.33400 zmin,zma (A): -23.52300 29.14100 x,y,z range (A): 42.82500 44.63300 52.66400 scale (grids/A): 0.6759835 object centre (A): -19.51550 -9.982500 2.808999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.8980 centred at (gu) : 89.93116 88.85063 88.76159 assigned negative charge : -301.3981 centred at (gu) : 89.74449 88.67269 88.69439 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6059 nv = 96 ne = 84 npr = 42443 no. pairs analyzed = 42443 no. exposed pairs = 2469 no. arc points = 17535 no. surface atoms = 836 nbur = 1158 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3337 m= 5 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2400000 number of dielectric boundary points 3039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1600 ## 137 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6958 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1270524E-08 4.8759001E-09 midg,1,midg; midg,igrid,midg -6.3723775E-08 2.4429147E-08 1,midg,midg; igrid,midg,midg -5.3028490E-08 3.2536349E-08 gauss-seidel spectral radius is 0.9885977 estimated iterations to convergence 76 setup time was (sec) 0.5000000 now iterating at: 07:05:13 rms-change max change #iterations 0.1634166 26.66457 at 10iterations 1.8509345E-02 2.748356 at 20iterations 2.0076314E-03 0.2742167 at 30iterations 2.2300094E-04 4.0596008E-02 at 40iterations 2.5175123E-05 3.5934448E-03 at 50iterations finished qdiffx linear iterations at : 07:05:16 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 2.5175123E-05 3.5934448E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 07:05:17 3.746u 0.378s 0:04.43 92.7% 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 Sun Oct 9 2011 at 07:05:17 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.027951 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): -40.92800 1.897000 ymin,ymax (A): -32.29900 12.33400 zmin,zma (A): -23.52300 29.14100 x,y,z range (A): 42.82500 44.63300 52.66400 scale (grids/A): 2.027951 object centre (A): -19.51550 -9.982500 2.808999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.8980 centred at (gu) : 89.79365 86.55202 86.28469 assigned negative charge : -301.3981 centred at (gu) : 89.23341 86.01814 86.08315 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17535 grid for indexing accessible points = 1.400000 m= 23849 mr = 44970 m= 4060 mr = 17630 m= 352 mr = 2598 m= 9 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 679 time to turn everything in is 0.5200000 number of dielectric boundary points 28138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14691 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) : 0.6759835 object centre at (A) : -19.51550 -9.982500 2.808999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5605289E-02 3.2293364E-02 midg,1,midg; midg,igrid,midg -3.4306619E-02 1.2843469E-02 1,midg,midg; igrid,midg,midg -3.4782145E-02 2.1788239E-02 gauss-seidel spectral radius is 0.9987254 estimated iterations to convergence 222 setup time was (sec) 0.8000000 now iterating at: 07:05:18 rms-change max change #iterations 4.221035 201.6704 at 10iterations 2.014970 82.41794 at 20iterations 0.9673907 32.18854 at 30iterations 0.4626729 16.52673 at 40iterations 0.2225856 7.975876 at 50iterations 0.1070137 3.567801 at 60iterations 5.1219467E-02 1.668316 at 70iterations 2.4713427E-02 0.7943249 at 80iterations 1.1772796E-02 0.4147415 at 90iterations 5.6854356E-03 0.1825390 at 100iterations 2.7315381E-03 8.7882757E-02 at 110iterations 1.3128620E-03 4.4704437E-02 at 120iterations finished qdiffx linear iterations at : 07:05:26 total time elapsed so far: 8.520000 # loops : 120 mean,max change (kT/e) : 1.3128620E-03 4.4704437E-02 energy calculations done at 8.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.690000 DelPhi exited at 07:05:26 8.694u 0.453s 0:09.41 97.1% 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 Sun Oct 9 2011 at 07:05:26 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 3.041926 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): -40.92800 1.897000 ymin,ymax (A): -32.29900 12.33400 zmin,zma (A): -23.52300 29.14100 x,y,z range (A): 42.82500 44.63300 52.66400 scale (grids/A): 3.041926 object centre (A): -19.51550 -9.982500 2.808999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.8980 centred at (gu) : 89.69040 84.82819 84.42677 assigned negative charge : -301.3981 centred at (gu) : 88.85015 84.02719 84.12486 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 150362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17535 grid for indexing accessible points = 1.400000 m= 76334 mr = 108390 m= 28523 mr = 62742 m= 7582 mr = 23171 m= 1383 mr = 5782 m= 188 mr = 892 m= 7 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 2270 time to turn everything in is 1.390000 number of dielectric boundary points 63297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 14840 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) : 2.027951 object centre at (A) : -19.51550 -9.982500 2.808999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5781625 0.9215052 midg,1,midg; midg,igrid,midg -0.2584012 0.1357431 1,midg,midg; igrid,midg,midg -0.3100796 0.1858018 gauss-seidel spectral radius is 0.9992660 estimated iterations to convergence 291 setup time was (sec) 1.680000 now iterating at: 07:05:28 rms-change max change #iterations 9.573643 438.7682 at 10iterations 5.507595 117.4571 at 20iterations 3.183108 63.91600 at 30iterations 1.832586 37.72197 at 40iterations 1.057030 19.30745 at 50iterations 0.6077608 11.68349 at 60iterations 0.3496604 6.299277 at 70iterations 0.2007660 4.064529 at 80iterations 0.1155789 2.248152 at 90iterations 6.6628866E-02 1.221611 at 100iterations 3.8145054E-02 0.8625834 at 110iterations 2.1977335E-02 0.4211464 at 120iterations 1.2625176E-02 0.2423172 at 130iterations 7.2769113E-03 0.1355352 at 140iterations 4.1792188E-03 8.7899685E-02 at 150iterations 2.4022767E-03 4.5707703E-02 at 160iterations 1.3820842E-03 2.5114292E-02 at 170iterations 7.9234858E-04 1.6297340E-02 at 180iterations finished qdiffx linear iterations at : 07:05:42 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 7.9234858E-04 1.6297340E-02 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 07:05:43 15.541u 0.477s 0:16.41 97.5% 0+0k 0+0io 0pf+0w