Mon Oct 10 14:36:49 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 Mon Oct 10 2011 at 14:36:49 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: ADP 651 has a net charge of -2.0000 !!! WARNING: MG6 652 has a net charge of 1.4000 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: 0.4201036 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): -5.681000 48.70600 ymin,ymax (A): 16.10000 100.8410 zmin,zma (A): 14.75900 72.72600 x,y,z range (A): 54.38700 84.74100 57.96700 scale (grids/A): 0.4201036 object centre (A): 21.51250 58.47050 43.74250 number of atom coordinates read : 2667 total number of charged atoms : 2518 net assigned charge : -4.599990 assigned positive charge : 410.1636 centred at (gu) : 88.95448 96.76433 88.98248 assigned negative charge : -414.7643 centred at (gu) : 89.02032 96.71181 89.01634 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 2839 nv = 96 ne = 84 npr = 51732 no. pairs analyzed = 51732 no. exposed pairs = 3741 no. arc points = 26199 no. surface atoms = 1260 nbur = 1407 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 = 1.988000 m= 70 mr = 1199 m= 0 mr = 0 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 1710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2122 ## 506 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 3918 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2211799E-13 -6.8949311E-13 midg,1,midg; midg,igrid,midg -1.5251433E-13 1.6707512E-12 1,midg,midg; igrid,midg,midg 4.3213604E-13 -9.7743460E-13 gauss-seidel spectral radius is 0.9710160 estimated iterations to convergence 49 setup time was (sec) 0.3800000 now iterating at: 14:36:50 rms-change max change #iterations 1.7451376E-02 5.226446 at 10iterations 5.7332212E-04 0.1379452 at 20iterations 4.2555039E-05 1.1165619E-02 at 30iterations 5.4803177E-06 1.4572144E-03 at 40iterations 7.7107597E-07 2.0599365E-04 at 50iterations finished qdiffx linear iterations at : 14:36:53 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 7.7107597E-07 2.0599365E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 14:36:54 3.533u 0.161s 0:04.23 87.2% 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 14:36:54 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: ADP 651 has a net charge of -2.0000 !!! WARNING: MG6 652 has a net charge of 1.4000 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: 1.260311 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): -5.681000 48.70600 ymin,ymax (A): 16.10000 100.8410 zmin,zma (A): 14.75900 72.72600 x,y,z range (A): 54.38700 84.74100 57.96700 scale (grids/A): 1.260311 object centre (A): 21.51250 58.47050 43.74250 number of atom coordinates read : 2667 total number of charged atoms : 2518 net assigned charge : -4.599990 assigned positive charge : 410.1636 centred at (gu) : 86.86267 110.2921 86.94705 assigned negative charge : -414.7643 centred at (gu) : 87.06044 110.1350 87.04863 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 32878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26199 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 7010 mr = 20250 m= 317 mr = 3752 m= 5 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 16149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 529 ## 18 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 17246 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) : 0.4201036 object centre at (A) : 21.51250 58.47050 43.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9521804E-04 8.2201802E-04 midg,1,midg; midg,igrid,midg -7.2397692E-03 -9.3149310E-03 1,midg,midg; igrid,midg,midg -5.5916916E-04 -6.9736881E-04 gauss-seidel spectral radius is 0.9967802 estimated iterations to convergence 141 setup time was (sec) 0.4000000 now iterating at: 14:36:54 rms-change max change #iterations 1.693034 188.4660 at 10iterations 0.5259899 43.25833 at 20iterations 0.1623338 12.12474 at 30iterations 5.0777197E-02 3.649467 at 40iterations 1.5801979E-02 0.8455410 at 50iterations 4.9538654E-03 0.2758623 at 60iterations 1.5583984E-03 8.9080811E-02 at 70iterations 4.9294700E-04 2.5669098E-02 at 80iterations 1.6335354E-04 1.0865211E-02 at 90iterations 5.8260008E-05 3.4027100E-03 at 100iterations 2.3754230E-05 1.3837814E-03 at 110iterations 1.1132954E-05 6.1416626E-04 at 120iterations finished qdiffx linear iterations at : 14:37:01 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 1.1132954E-05 6.1416626E-04 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.280000 DelPhi exited at 14:37:02 7.286u 0.207s 0:08.09 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 Mon Oct 10 2011 at 14:37:02 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: ADP 651 has a net charge of -2.0000 !!! WARNING: MG6 652 has a net charge of 1.4000 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: 1.890466 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): -5.681000 48.70600 ymin,ymax (A): 16.10000 100.8410 zmin,zma (A): 14.75900 72.72600 x,y,z range (A): 54.38700 84.74100 57.96700 scale (grids/A): 1.890466 object centre (A): 21.51250 58.47050 43.74250 number of atom coordinates read : 2667 total number of charged atoms : 2518 net assigned charge : -4.599990 assigned positive charge : 410.1636 centred at (gu) : 85.29393 120.4384 85.42039 assigned negative charge : -414.7643 centred at (gu) : 85.59060 120.2025 85.57287 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26199 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 27284 mr = 50835 m= 4472 mr = 18977 m= 274 mr = 2578 m= 5 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 36439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 19811 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) : 1.260311 object centre at (A) : 21.51250 58.47050 43.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8398009E-02 2.6410155E-02 midg,1,midg; midg,igrid,midg -0.1324112 -0.1766777 1,midg,midg; igrid,midg,midg -1.6548323E-02 -9.9161994E-03 gauss-seidel spectral radius is 0.9985529 estimated iterations to convergence 208 setup time was (sec) 0.6200000 now iterating at: 14:37:03 rms-change max change #iterations 5.166924 270.3103 at 10iterations 2.428159 104.8740 at 20iterations 1.134591 54.90085 at 30iterations 0.5278665 19.13054 at 40iterations 0.2451365 8.345032 at 50iterations 0.1127664 3.736446 at 60iterations 5.1969297E-02 1.825523 at 70iterations 2.3993939E-02 0.7829227 at 80iterations 1.1043053E-02 0.3833513 at 90iterations 5.0745429E-03 0.1638302 at 100iterations 2.3406229E-03 7.4645519E-02 at 110iterations 1.0734524E-03 3.4362793E-02 at 120iterations 4.9337366E-04 1.5182495E-02 at 130iterations 2.2861749E-04 8.1369877E-03 at 140iterations 1.0558303E-04 3.8812160E-03 at 150iterations 4.9407365E-05 1.5439987E-03 at 160iterations 2.3488803E-05 7.8964233E-04 at 170iterations 1.1470644E-05 3.6287308E-04 at 180iterations finished qdiffx linear iterations at : 14:37:13 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 1.1470644E-05 3.6287308E-04 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 14:37:14 11.258u 0.261s 0:12.02 95.7% 0+0k 0+0io 0pf+0w