Tue Oct 11 06:11:42 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 06:11:42 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 = 2030 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7312164 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): 20.18500 64.35300 ymin,ymax (A): -3.419000 34.97000 zmin,zma (A): 22.96600 71.65200 x,y,z range (A): 44.16800 38.38900 48.68600 scale (grids/A): 0.7312164 object centre (A): 42.26900 15.77550 47.30900 number of atom coordinates read : 2030 total number of charged atoms : 1900 net assigned charge : 4.500006 assigned positive charge : 305.6701 centred at (gu) : 89.87047 89.05505 88.50111 assigned negative charge : -301.1702 centred at (gu) : 90.02486 89.16798 88.48994 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7470 nv = 96 ne = 84 npr = 40777 no. pairs analyzed = 40777 no. exposed pairs = 2486 no. arc points = 16980 no. surface atoms = 848 nbur = 1182 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 604 mr = 4384 m= 7 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1420 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2897627E-08 5.5818870E-08 midg,1,midg; midg,igrid,midg 1.8340124E-07 -2.1364706E-08 1,midg,midg; igrid,midg,midg 1.9001568E-07 -5.8637738E-08 gauss-seidel spectral radius is 0.9902416 estimated iterations to convergence 82 setup time was (sec) 0.5200000 now iterating at: 06:11:43 rms-change max change #iterations 0.2305034 28.76171 at 10iterations 3.0850343E-02 4.365334 at 20iterations 4.1649216E-03 0.5860615 at 30iterations 6.7619636E-04 7.8399658E-02 at 40iterations 1.5303175E-04 1.7833710E-02 at 50iterations finished qdiffx linear iterations at : 06:11:46 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 1.5303175E-04 1.7833710E-02 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 06:11:47 4.106u 0.239s 0:04.63 93.5% 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 06:11:47 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 = 2030 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.193649 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): 20.18500 64.35300 ymin,ymax (A): -3.419000 34.97000 zmin,zma (A): 22.96600 71.65200 x,y,z range (A): 44.16800 38.38900 48.68600 scale (grids/A): 2.193649 object centre (A): 42.26900 15.77550 47.30900 number of atom coordinates read : 2030 total number of charged atoms : 1900 net assigned charge : 4.500006 assigned positive charge : 305.6701 centred at (gu) : 89.61145 87.16546 85.50336 assigned negative charge : -301.1702 centred at (gu) : 90.07486 87.50391 85.46999 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16980 grid for indexing accessible points = 1.400000 m= 33654 mr = 56269 m= 7570 mr = 25878 m= 861 mr = 5254 m= 21 mr = 470 m= 0 mr = 4 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 32936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15122 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) : 0.7312164 object centre at (A) : 42.26900 15.77550 47.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5475523E-04 2.4262765E-02 midg,1,midg; midg,igrid,midg 3.8640980E-02 -5.8607245E-03 1,midg,midg; igrid,midg,midg 5.2958485E-02 2.7350767E-02 gauss-seidel spectral radius is 0.9988906 estimated iterations to convergence 238 setup time was (sec) 0.9800000 now iterating at: 06:11:48 rms-change max change #iterations 4.782061 183.1474 at 10iterations 2.409199 79.63121 at 20iterations 1.221473 38.14261 at 30iterations 0.6193284 18.24580 at 40iterations 0.3132097 8.647392 at 50iterations 0.1583106 4.386136 at 60iterations 8.0391489E-02 2.361702 at 70iterations 4.0745918E-02 1.256681 at 80iterations 2.0631449E-02 0.6278653 at 90iterations 1.0498106E-02 0.3257284 at 100iterations 5.3723427E-03 0.1479912 at 110iterations 2.7811273E-03 8.2798004E-02 at 120iterations finished qdiffx linear iterations at : 06:11:57 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 2.7811273E-03 8.2798004E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.950000 DelPhi exited at 06:11:57 9.955u 0.264s 0:10.50 97.2% 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 Tue Oct 11 2011 at 06:11:57 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 = 2030 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: 3.290474 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): 20.18500 64.35300 ymin,ymax (A): -3.419000 34.97000 zmin,zma (A): 22.96600 71.65200 x,y,z range (A): 44.16800 38.38900 48.68600 scale (grids/A): 3.290474 object centre (A): 42.26900 15.77550 47.30900 number of atom coordinates read : 2030 total number of charged atoms : 1900 net assigned charge : 4.500006 assigned positive charge : 305.6701 centred at (gu) : 89.41730 85.74818 83.25497 assigned negative charge : -301.1702 centred at (gu) : 90.11230 86.25585 83.20498 start vw surface at 0.1300000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 181097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16980 grid for indexing accessible points = 1.400000 m= 101905 mr = 134936 m= 45216 mr = 85483 m= 14741 mr = 37672 m= 3252 mr = 11676 m= 433 mr = 2374 m= 26 mr = 317 m= 0 mr = 8 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 74204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 15192 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) : 2.193649 object centre at (A) : 42.26900 15.77550 47.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3119959E-02 -0.1092454 midg,1,midg; midg,igrid,midg 0.2902606 -3.0808479E-02 1,midg,midg; igrid,midg,midg 0.4349001 0.4397174 gauss-seidel spectral radius is 0.9993120 estimated iterations to convergence 301 setup time was (sec) 2.350000 now iterating at: 06:12:00 rms-change max change #iterations 10.60095 359.5981 at 10iterations 6.349089 125.1179 at 20iterations 3.805801 74.60571 at 30iterations 2.267277 43.99691 at 40iterations 1.350331 25.70280 at 50iterations 0.7993423 14.50633 at 60iterations 0.4743000 8.145357 at 70iterations 0.2801676 5.291466 at 80iterations 0.1658240 3.094620 at 90iterations 9.7725242E-02 1.776519 at 100iterations 5.7935279E-02 0.9639215 at 110iterations 3.4344722E-02 0.5813332 at 120iterations 2.0460367E-02 0.3516083 at 130iterations 1.2347141E-02 0.2305193 at 140iterations 7.5917481E-03 0.1304283 at 150iterations 4.8224265E-03 8.3864212E-02 at 160iterations 3.2239866E-03 5.5099487E-02 at 170iterations 2.3013344E-03 3.7227631E-02 at 180iterations finished qdiffx linear iterations at : 06:12:13 total time elapsed so far: 15.79000 # loops : 180 mean,max change (kT/e) : 2.3013344E-03 3.7227631E-02 energy calculations done at 15.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.97000 DelPhi exited at 06:12:14 15.975u 0.269s 0:16.54 98.1% 0+0k 0+0io 0pf+0w