Sat Oct 8 16:47:31 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 Sat Oct 8 2011 at 16:47:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4469 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: 0.5466159 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): 16.00000 79.22000 ymin,ymax (A): 118.7120 183.8400 zmin,zma (A): -1.078000 59.81000 x,y,z range (A): 63.22000 65.12800 60.88800 scale (grids/A): 0.5466159 object centre (A): 47.61000 151.2760 29.36600 number of atom coordinates read : 4469 total number of charged atoms : 4299 net assigned charge : 4.500037 assigned positive charge : 684.3987 centred at (gu) : 91.78476 89.69794 87.54894 assigned negative charge : -679.9019 centred at (gu) : 91.77187 89.63328 87.58372 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8475 nv = 96 ne = 84 npr = 90684 no. pairs analyzed = 90684 no. exposed pairs = 5449 no. arc points = 37126 no. surface atoms = 1826 nbur = 2643 mkacc time = 0.2300000 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= 345 mr = 4545 m= 0 mr = 22 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3891 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11390 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1623358E-09 -4.2149974E-11 midg,1,midg; midg,igrid,midg -4.2920581E-10 8.6626489E-10 1,midg,midg; igrid,midg,midg 9.4163947E-11 6.3000238E-10 gauss-seidel spectral radius is 0.9828508 estimated iterations to convergence 63 setup time was (sec) 0.8300000 now iterating at: 16:47:32 rms-change max change #iterations 9.2457481E-02 13.68995 at 10iterations 6.8227318E-03 0.9741745 at 20iterations 1.0466842E-03 0.1555004 at 30iterations 3.3311191E-04 4.8532486E-02 at 40iterations 1.2027667E-04 1.6141891E-02 at 50iterations finished qdiffx linear iterations at : 16:47:37 total time elapsed so far: 5.210000 # loops : 50 mean,max change (kT/e) : 1.2027667E-04 1.6141891E-02 energy calculations done at 5.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.370000 DelPhi exited at 16:47:37 5.371u 0.451s 0:06.16 94.4% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 16:47:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4469 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.639848 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): 16.00000 79.22000 ymin,ymax (A): 118.7120 183.8400 zmin,zma (A): -1.078000 59.81000 x,y,z range (A): 63.22000 65.12800 60.88800 scale (grids/A): 1.639848 object centre (A): 47.61000 151.2760 29.36600 number of atom coordinates read : 4469 total number of charged atoms : 4299 net assigned charge : 4.500037 assigned positive charge : 684.3987 centred at (gu) : 95.35340 89.09257 82.64574 assigned negative charge : -679.9019 centred at (gu) : 95.31534 88.89962 82.75082 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 95190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37126 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29766 mr = 66770 m= 3386 mr = 20216 m= 102 mr = 1787 m= 0 mr = 6 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 398 time to turn everything in is 0.8000000 number of dielectric boundary points 39665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 505 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 32966 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) : 0.5466159 object centre at (A) : 47.61000 151.2760 29.36600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7489400E-03 7.8921616E-03 midg,1,midg; midg,igrid,midg 1.2683350E-02 2.8602652E-02 1,midg,midg; igrid,midg,midg -1.1454067E-02 -1.3871098E-02 gauss-seidel spectral radius is 0.9983421 estimated iterations to convergence 195 setup time was (sec) 1.140000 now iterating at: 16:47:39 rms-change max change #iterations 4.240104 153.3408 at 10iterations 1.832415 58.69603 at 20iterations 0.7950719 27.65495 at 30iterations 0.3452165 10.44647 at 40iterations 0.1497538 5.121811 at 50iterations 6.5107681E-02 1.906906 at 60iterations 2.8315334E-02 0.9025116 at 70iterations 1.2381586E-02 0.3772659 at 80iterations 5.4654931E-03 0.1722488 at 90iterations 2.4534049E-03 8.5637808E-02 at 100iterations 1.1485917E-03 3.4915924E-02 at 110iterations 5.7216390E-04 1.7597198E-02 at 120iterations finished qdiffx linear iterations at : 16:47:50 total time elapsed so far: 12.63000 # loops : 120 mean,max change (kT/e) : 5.7216390E-04 1.7597198E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 16:47:51 12.804u 0.547s 0:13.63 97.8% 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 Sat Oct 8 2011 at 16:47:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4469 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: 2.459772 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): 16.00000 79.22000 ymin,ymax (A): 118.7120 183.8400 zmin,zma (A): -1.078000 59.81000 x,y,z range (A): 63.22000 65.12800 60.88800 scale (grids/A): 2.459772 object centre (A): 47.61000 151.2760 29.36600 number of atom coordinates read : 4469 total number of charged atoms : 4299 net assigned charge : 4.500037 assigned positive charge : 684.3987 centred at (gu) : 98.02976 88.63863 78.96818 assigned negative charge : -679.9019 centred at (gu) : 97.97277 88.34921 79.12612 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 221719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37126 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 103419 mr = 163585 m= 29851 mr = 81778 m= 5467 mr = 22155 m= 443 mr = 3857 m= 5 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 1400 time to turn everything in is 2.010000 number of dielectric boundary points 89328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 34337 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) : 1.639848 object centre at (A) : 47.61000 151.2760 29.36600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6508252E-03 0.1719593 midg,1,midg; midg,igrid,midg 0.2162400 0.4629030 1,midg,midg; igrid,midg,midg -0.1703250 -0.2487570 gauss-seidel spectral radius is 0.9992167 estimated iterations to convergence 282 setup time was (sec) 2.430000 now iterating at: 16:47:54 rms-change max change #iterations 11.03734 294.2471 at 10iterations 6.430792 128.6023 at 20iterations 3.711765 80.91203 at 30iterations 2.140756 39.54433 at 40iterations 1.226989 22.33176 at 50iterations 0.7010615 13.75450 at 60iterations 0.3998308 7.470034 at 70iterations 0.2274377 3.872296 at 80iterations 0.1294010 2.157843 at 90iterations 7.3470347E-02 1.267309 at 100iterations 4.1670822E-02 0.7278404 at 110iterations 2.3717476E-02 0.4262085 at 120iterations 1.3474351E-02 0.2484200 at 130iterations 7.6282062E-03 0.1450214 at 140iterations 4.3449360E-03 7.0931435E-02 at 150iterations 2.4747623E-03 4.1687012E-02 at 160iterations 1.4181725E-03 2.3567200E-02 at 170iterations 8.1926706E-04 1.4081955E-02 at 180iterations finished qdiffx linear iterations at : 16:48:14 total time elapsed so far: 22.01000 # loops : 180 mean,max change (kT/e) : 8.1926706E-04 1.4081955E-02 energy calculations done at 22.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.18000 DelPhi exited at 16:48:14 22.183u 0.558s 0:23.05 98.6% 0+0k 0+0io 0pf+0w