Tue Oct 11 04:12:03 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 Tue Oct 11 2011 at 04:12:03 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6434239 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): -9.511000 35.92300 ymin,ymax (A): -26.81300 21.67700 zmin,zma (A): -10.11000 45.21900 x,y,z range (A): 45.43400 48.49000 55.32900 scale (grids/A): 0.6434239 object centre (A): 13.20600 -2.568000 17.55450 number of atom coordinates read : 2762 total number of charged atoms : 2634 net assigned charge : 3.162012 assigned positive charge : 421.2396 centred at (gu) : 89.73615 90.53954 91.70373 assigned negative charge : -418.0783 centred at (gu) : 89.48151 90.40608 91.67815 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7539 nv = 96 ne = 84 npr = 55622 no. pairs analyzed = 55622 no. exposed pairs = 3440 no. arc points = 23526 no. surface atoms = 1157 nbur = 1605 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 4200 m= 5 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3200000 number of dielectric boundary points 3689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2328 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1262375E-09 1.2285775E-08 midg,1,midg; midg,igrid,midg -1.2036072E-08 2.5975144E-08 1,midg,midg; igrid,midg,midg -3.2781632E-08 3.6936573E-08 gauss-seidel spectral radius is 0.9874947 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 04:12:04 rms-change max change #iterations 0.1555518 27.23772 at 10iterations 1.5854569E-02 2.482542 at 20iterations 1.6031223E-03 0.2303169 at 30iterations 1.6752127E-04 2.6093483E-02 at 40iterations 1.8653582E-05 2.2735596E-03 at 50iterations finished qdiffx linear iterations at : 04:12:07 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.8653582E-05 2.2735596E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 04:12:07 3.330u 0.134s 0:03.95 87.5% 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 Tue Oct 11 2011 at 04:12:07 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.930272 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): -9.511000 35.92300 ymin,ymax (A): -26.81300 21.67700 zmin,zma (A): -10.11000 45.21900 x,y,z range (A): 45.43400 48.49000 55.32900 scale (grids/A): 1.930272 object centre (A): 13.20600 -2.568000 17.55450 number of atom coordinates read : 2762 total number of charged atoms : 2634 net assigned charge : 3.162012 assigned positive charge : 421.2396 centred at (gu) : 89.20756 91.61819 95.11044 assigned negative charge : -418.0783 centred at (gu) : 88.44422 91.21774 95.03414 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81631 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23526 grid for indexing accessible points = 1.400000 m= 29867 mr = 57348 m= 4670 mr = 22067 m= 256 mr = 2869 m= 1 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 376 time to turn everything in is 0.5600000 number of dielectric boundary points 34058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 20746 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) : 0.6434239 object centre at (A) : 13.20600 -2.568000 17.55450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9695874E-03 7.3727565E-03 midg,1,midg; midg,igrid,midg -1.6458021E-02 7.7224071E-03 1,midg,midg; igrid,midg,midg -1.5582820E-02 5.5177338E-02 gauss-seidel spectral radius is 0.9986848 estimated iterations to convergence 218 setup time was (sec) 0.8300000 now iterating at: 04:12:08 rms-change max change #iterations 4.536234 184.5313 at 10iterations 2.157051 72.63748 at 20iterations 1.027280 31.39401 at 30iterations 0.4885203 14.88118 at 40iterations 0.2322853 7.325970 at 50iterations 0.1106805 3.436993 at 60iterations 5.2632194E-02 1.697027 at 70iterations 2.5073800E-02 0.8100891 at 80iterations 1.1911878E-02 0.3579807 at 90iterations 5.6727668E-03 0.1800213 at 100iterations 2.6890358E-03 7.8762054E-02 at 110iterations 1.2851586E-03 3.7053108E-02 at 120iterations finished qdiffx linear iterations at : 04:12:14 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 1.2851586E-03 3.7053108E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 04:12:15 7.016u 0.174s 0:07.72 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 Tue Oct 11 2011 at 04:12:15 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.895407 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): -9.511000 35.92300 ymin,ymax (A): -26.81300 21.67700 zmin,zma (A): -10.11000 45.21900 x,y,z range (A): 45.43400 48.49000 55.32900 scale (grids/A): 2.895407 object centre (A): 13.20600 -2.568000 17.55450 number of atom coordinates read : 2762 total number of charged atoms : 2634 net assigned charge : 3.162012 assigned positive charge : 421.2396 centred at (gu) : 88.81114 92.42700 97.66549 assigned negative charge : -418.0783 centred at (gu) : 87.66628 91.82667 97.55106 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 188794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23526 grid for indexing accessible points = 1.400000 m= 96508 mr = 138873 m= 35147 mr = 79152 m= 8393 mr = 28148 m= 1098 mr = 6242 m= 53 mr = 682 m= 0 mr = 19 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1381 time to turn everything in is 1.530000 number of dielectric boundary points 76877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 21050 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) : 1.930272 object centre at (A) : 13.20600 -2.568000 17.55450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2670087 0.2652826 midg,1,midg; midg,igrid,midg -0.1844634 2.0415394E-02 1,midg,midg; igrid,midg,midg -8.6548857E-02 0.4654351 gauss-seidel spectral radius is 0.9992703 estimated iterations to convergence 292 setup time was (sec) 1.810000 now iterating at: 04:12:17 rms-change max change #iterations 10.52580 365.1289 at 10iterations 6.170887 131.1972 at 20iterations 3.608719 66.30431 at 30iterations 2.103554 43.02322 at 40iterations 1.221554 21.95883 at 50iterations 0.7111396 12.75874 at 60iterations 0.4122459 7.221581 at 70iterations 0.2390890 4.436937 at 80iterations 0.1384765 2.719594 at 90iterations 8.0091067E-02 1.514186 at 100iterations 4.6376850E-02 0.9497604 at 110iterations 2.6833137E-02 0.4667149 at 120iterations 1.5496449E-02 0.3005829 at 130iterations 8.9887781E-03 0.1538858 at 140iterations 5.2025765E-03 9.3658447E-02 at 150iterations 3.0155787E-03 5.0716400E-02 at 160iterations 1.7589348E-03 3.0318260E-02 at 170iterations 1.0264872E-03 1.7528534E-02 at 180iterations finished qdiffx linear iterations at : 04:12:27 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 1.0264872E-03 1.7528534E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 04:12:27 11.555u 0.190s 0:12.17 96.4% 0+0k 0+0io 0pf+0w