Sat Oct 8 23:13:49 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+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 Sat Oct 8 2011 at 23:13:49 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2453 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6432030 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): 0.3140000 54.79700 ymin,ymax (A): 19.97300 63.45700 zmin,zma (A): -11.96600 43.38200 x,y,z range (A): 54.48300 43.48400 55.34800 scale (grids/A): 0.6432030 object centre (A): 27.55550 41.71500 15.70800 number of atom coordinates read : 2453 total number of charged atoms : 2317 net assigned charge : 11.51402 assigned positive charge : 361.5262 centred at (gu) : 89.54300 89.55012 90.59360 assigned negative charge : -350.0130 centred at (gu) : 89.56325 89.63292 90.56113 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6928 nv = 96 ne = 84 npr = 48946 no. pairs analyzed = 48946 no. exposed pairs = 3339 no. arc points = 23785 no. surface atoms = 1112 nbur = 1341 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 3544 m= 2 mr = 58 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 0.1800000 number of dielectric boundary points 3761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2323 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2901685E-08 2.4887767E-08 midg,1,midg; midg,igrid,midg 3.0442312E-08 7.9762872E-09 1,midg,midg; igrid,midg,midg 2.2647527E-08 1.4538607E-08 gauss-seidel spectral radius is 0.9874726 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 23:13:49 rms-change max change #iterations 0.1421061 25.26493 at 10iterations 1.4087033E-02 2.145126 at 20iterations 1.4999325E-03 0.2445107 at 30iterations 2.2297286E-04 3.8368225E-02 at 40iterations 5.9736627E-05 1.2484550E-02 at 50iterations finished qdiffx linear iterations at : 23:13:53 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.9736627E-05 1.2484550E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 23:13:53 3.558u 0.215s 0:04.03 93.3% 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 23:13:53 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2453 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.929609 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): 0.3140000 54.79700 ymin,ymax (A): 19.97300 63.45700 zmin,zma (A): -11.96600 43.38200 x,y,z range (A): 54.48300 43.48400 55.34800 scale (grids/A): 1.929609 object centre (A): 27.55550 41.71500 15.70800 number of atom coordinates read : 2453 total number of charged atoms : 2317 net assigned charge : 11.51402 assigned positive charge : 361.5262 centred at (gu) : 88.62871 88.65003 91.78045 assigned negative charge : -350.0130 centred at (gu) : 88.68987 88.89871 91.68358 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23785 grid for indexing accessible points = 1.400000 m= 27267 mr = 48875 m= 4941 mr = 19321 m= 365 mr = 3001 m= 10 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 335 time to turn everything in is 0.3800000 number of dielectric boundary points 34988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 18251 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) : 0.6432030 object centre at (A) : 27.55550 41.71500 15.70800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6544719E-02 3.3243865E-02 midg,1,midg; midg,igrid,midg 3.1570364E-02 4.3646698E-03 1,midg,midg; igrid,midg,midg 5.4200370E-02 1.6214108E-02 gauss-seidel spectral radius is 0.9986692 estimated iterations to convergence 217 setup time was (sec) 0.6400000 now iterating at: 23:13:54 rms-change max change #iterations 4.143223 209.2738 at 10iterations 1.954154 74.52745 at 20iterations 0.9252134 29.95039 at 30iterations 0.4357576 14.67188 at 40iterations 0.2053075 6.298405 at 50iterations 9.7042620E-02 3.305276 at 60iterations 4.5781817E-02 1.401955 at 70iterations 2.1619564E-02 0.6858447 at 80iterations 1.0268481E-02 0.3534403 at 90iterations 4.8517925E-03 0.1612797 at 100iterations 2.3097463E-03 7.2921753E-02 at 110iterations 1.1126172E-03 3.8795471E-02 at 120iterations finished qdiffx linear iterations at : 23:14:02 total time elapsed so far: 8.400000 # loops : 120 mean,max change (kT/e) : 1.1126172E-03 3.8795471E-02 energy calculations done at 8.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 23:14:02 8.531u 0.236s 0:09.17 95.5% 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 Sat Oct 8 2011 at 23:14:02 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2453 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.894413 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): 0.3140000 54.79700 ymin,ymax (A): 19.97300 63.45700 zmin,zma (A): -11.96600 43.38200 x,y,z range (A): 54.48300 43.48400 55.34800 scale (grids/A): 2.894413 object centre (A): 27.55550 41.71500 15.70800 number of atom coordinates read : 2453 total number of charged atoms : 2317 net assigned charge : 11.51402 assigned positive charge : 361.5262 centred at (gu) : 87.94280 87.97497 92.67064 assigned negative charge : -350.0130 centred at (gu) : 88.03474 88.34796 92.52534 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23785 grid for indexing accessible points = 1.400000 m= 85372 mr = 119249 m= 33017 mr = 67984 m= 9111 mr = 25966 m= 1567 mr = 6578 m= 119 mr = 1043 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1105 time to turn everything in is 0.9700000 number of dielectric boundary points 78929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 18535 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) : 1.929609 object centre at (A) : 27.55550 41.71500 15.70800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6613232 0.3645606 midg,1,midg; midg,igrid,midg 0.3043835 2.4384703E-02 1,midg,midg; igrid,midg,midg 0.5188799 0.1305917 gauss-seidel spectral radius is 0.9992779 estimated iterations to convergence 294 setup time was (sec) 1.220000 now iterating at: 23:14:04 rms-change max change #iterations 9.879332 340.0466 at 10iterations 5.880741 142.3416 at 20iterations 3.478388 71.82120 at 30iterations 2.042274 46.83764 at 40iterations 1.195934 25.32339 at 50iterations 0.6971077 13.38288 at 60iterations 0.4061294 7.834209 at 70iterations 0.2362970 4.569382 at 80iterations 0.1375018 2.609397 at 90iterations 7.9742156E-02 1.495983 at 100iterations 4.6234455E-02 0.8389053 at 110iterations 2.6860235E-02 0.5295808 at 120iterations 1.5562748E-02 0.2789383 at 130iterations 9.0313340E-03 0.1648102 at 140iterations 5.2203424E-03 0.1033654 at 150iterations 3.0329716E-03 5.8082581E-02 at 160iterations 1.7579405E-03 3.1897545E-02 at 170iterations 1.0226719E-03 1.7963409E-02 at 180iterations finished qdiffx linear iterations at : 23:14:15 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 1.0226719E-03 1.7963409E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 23:14:16 13.178u 0.216s 0:13.69 97.7% 0+0k 0+0io 0pf+0w