Sun Oct 9 15:18:51 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 Sun Oct 9 2011 at 15:18:51 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5737 !!! WARNING: HIR 555 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4994599 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): 67.29300 138.5700 ymin,ymax (A): -6.219000 57.05100 zmin,zma (A): -3.285000 66.32401 x,y,z range (A): 71.27699 63.27000 69.60901 scale (grids/A): 0.4994599 object centre (A): 102.9315 25.41600 31.51950 number of atom coordinates read : 5737 total number of charged atoms : 5566 net assigned charge : 1.514035 assigned positive charge : 880.1876 centred at (gu) : 89.73878 90.65225 90.08157 assigned negative charge : -878.6821 centred at (gu) : 89.79238 90.63059 90.17675 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8655 nv = 96 ne = 84 npr = 118959 no. pairs analyzed = 118959 no. exposed pairs = 6475 no. arc points = 45029 no. surface atoms = 2171 nbur = 3566 mkacc time = 0.2800000 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 = 1.708000 m= 288 mr = 4772 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.5600000 number of dielectric boundary points 4169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4316 ## 662 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 11897 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9259727E-10 -1.8068132E-10 midg,1,midg; midg,igrid,midg -2.5109711E-11 6.5569668E-11 1,midg,midg; igrid,midg,midg 1.2559609E-10 -8.6958413E-11 gauss-seidel spectral radius is 0.9795558 estimated iterations to convergence 58 setup time was (sec) 0.7900000 now iterating at: 15:18:52 rms-change max change #iterations 6.7629755E-02 10.28127 at 10iterations 4.5975829E-03 0.6635933 at 20iterations 7.7065791E-04 9.0119839E-02 at 30iterations 2.0514763E-04 2.4562836E-02 at 40iterations 6.0414735E-05 7.1887970E-03 at 50iterations finished qdiffx linear iterations at : 15:18:55 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 6.0414735E-05 7.1887970E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 15:18:55 3.644u 0.146s 0:04.09 92.4% 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 15:18:56 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5737 !!! WARNING: HIR 555 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.498380 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): 67.29300 138.5700 ymin,ymax (A): -6.219000 57.05100 zmin,zma (A): -3.285000 66.32401 x,y,z range (A): 71.27699 63.27000 69.60901 scale (grids/A): 1.498380 object centre (A): 102.9315 25.41600 31.51950 number of atom coordinates read : 5737 total number of charged atoms : 5566 net assigned charge : 1.514035 assigned positive charge : 880.1876 centred at (gu) : 89.21436 91.95499 90.24274 assigned negative charge : -878.6821 centred at (gu) : 89.37687 91.89172 90.53008 start vw surface at 0.2500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 100198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28039 mr = 71265 m= 2291 mr = 19136 m= 54 mr = 1016 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 4643 time to turn everything in is 0.7400000 number of dielectric boundary points 39165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 657 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 41556 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) : 0.4994599 object centre at (A) : 102.9315 25.41600 31.51950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1788494E-03 3.2956772E-03 midg,1,midg; midg,igrid,midg -1.1465388E-03 5.3517497E-03 1,midg,midg; igrid,midg,midg -1.4924021E-02 -5.3100940E-03 gauss-seidel spectral radius is 0.9980873 estimated iterations to convergence 182 setup time was (sec) 1.040000 now iterating at: 15:18:57 rms-change max change #iterations 4.075538 154.1089 at 10iterations 1.657266 54.82904 at 20iterations 0.6775601 19.75177 at 30iterations 0.2766639 8.716194 at 40iterations 0.1130839 3.445991 at 50iterations 4.6314266E-02 1.567938 at 60iterations 1.9073861E-02 0.5480877 at 70iterations 7.8664236E-03 0.2409725 at 80iterations 3.2758897E-03 0.1064491 at 90iterations 1.4006160E-03 4.7825813E-02 at 100iterations 6.3082803E-04 1.8319249E-02 at 110iterations 3.0769833E-04 8.9092255E-03 at 120iterations finished qdiffx linear iterations at : 15:19:03 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 3.0769833E-04 8.9092255E-03 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 15:19:04 7.998u 0.159s 0:08.43 96.5% 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 15:19:04 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5737 !!! WARNING: HIR 555 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.247570 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): 67.29300 138.5700 ymin,ymax (A): -6.219000 57.05100 zmin,zma (A): -3.285000 66.32401 x,y,z range (A): 71.27699 63.27000 69.60901 scale (grids/A): 2.247570 object centre (A): 102.9315 25.41600 31.51950 number of atom coordinates read : 5737 total number of charged atoms : 5566 net assigned charge : 1.514035 assigned positive charge : 880.1876 centred at (gu) : 88.82119 92.93185 90.36368 assigned negative charge : -878.6821 centred at (gu) : 89.06523 92.83770 90.79493 start vw surface at 0.2400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 234476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 103007 mr = 175200 m= 25127 mr = 81912 m= 3172 mr = 18450 m= 122 mr = 1891 m= 0 mr = 41 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 15273 time to turn everything in is 1.720000 number of dielectric boundary points 88410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 44374 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) : 1.498380 object centre at (A) : 102.9315 25.41600 31.51950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5115111E-02 0.1962984 midg,1,midg; midg,igrid,midg -4.9621619E-02 0.1632035 1,midg,midg; igrid,midg,midg -0.5157913 0.2042417 gauss-seidel spectral radius is 0.9991661 estimated iterations to convergence 273 setup time was (sec) 2.020000 now iterating at: 15:19:06 rms-change max change #iterations 11.03331 304.3506 at 10iterations 6.279983 129.8459 at 20iterations 3.560065 83.63231 at 30iterations 2.007307 38.87936 at 40iterations 1.129239 26.41826 at 50iterations 0.6330473 11.92541 at 60iterations 0.3545405 6.238965 at 70iterations 0.1981306 3.618539 at 80iterations 0.1105167 2.070387 at 90iterations 6.1781596E-02 1.107578 at 100iterations 3.4474861E-02 0.7496185 at 110iterations 1.9211572E-02 0.3654823 at 120iterations 1.0700349E-02 0.1849918 at 130iterations 5.9606158E-03 0.1052608 at 140iterations 3.3326421E-03 6.5613747E-02 at 150iterations 1.8585583E-03 3.3306122E-02 at 160iterations 1.0441757E-03 1.7190933E-02 at 170iterations 5.8869057E-04 1.0345221E-02 at 180iterations finished qdiffx linear iterations at : 15:19:17 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 5.8869057E-04 1.0345221E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 15:19:17 12.994u 0.195s 0:13.46 97.9% 0+0k 0+0io 0pf+0w