Mon Oct 10 16:19:52 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 16:19:52 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 = 4811 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5496371 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): -63.08800 -7.559000 ymin,ymax (A): -34.81000 29.63000 zmin,zma (A): -29.13400 35.63600 x,y,z range (A): 55.52900 64.44000 64.77000 scale (grids/A): 0.5496371 object centre (A): -35.32350 -2.590001 3.251001 number of atom coordinates read : 4811 total number of charged atoms : 4653 net assigned charge : 7.000030 assigned positive charge : 724.2505 centred at (gu) : 90.53220 89.95163 88.53995 assigned negative charge : -717.2551 centred at (gu) : 90.53939 89.98655 88.54401 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9334 nv = 96 ne = 84 npr = 98807 no. pairs analyzed = 98807 no. exposed pairs = 5833 no. arc points = 39165 no. surface atoms = 1957 nbur = 2854 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= 374 mr = 5159 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4063 ## 496 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12387 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8326567E-10 3.1964853E-10 midg,1,midg; midg,igrid,midg 9.3751840E-10 7.0171133E-11 1,midg,midg; igrid,midg,midg 5.1802368E-10 4.6773280E-10 gauss-seidel spectral radius is 0.9830620 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 16:19:53 rms-change max change #iterations 9.7142249E-02 13.04471 at 10iterations 7.2998200E-03 0.8890762 at 20iterations 1.3367549E-03 0.2070789 at 30iterations 5.5908982E-04 7.4298859E-02 at 40iterations 2.5732382E-04 3.4164429E-02 at 50iterations finished qdiffx linear iterations at : 16:19:55 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 2.5732382E-04 3.4164429E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 16:19:56 3.718u 0.162s 0:04.17 92.8% 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 Mon Oct 10 2011 at 16:19:56 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 = 4811 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.648911 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): -63.08800 -7.559000 ymin,ymax (A): -34.81000 29.63000 zmin,zma (A): -29.13400 35.63600 x,y,z range (A): 55.52900 64.44000 64.77000 scale (grids/A): 1.648911 object centre (A): -35.32350 -2.590001 3.251001 number of atom coordinates read : 4811 total number of charged atoms : 4653 net assigned charge : 7.000030 assigned positive charge : 724.2505 centred at (gu) : 91.59497 89.85334 85.61826 assigned negative charge : -717.2551 centred at (gu) : 91.61767 89.95940 85.63148 start vw surface at 0.2400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 104313 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39165 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33599 mr = 74250 m= 3721 mr = 23632 m= 103 mr = 1941 m= 0 mr = 16 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1782 time to turn everything in is 0.7900000 number of dielectric boundary points 41897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 453 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 35728 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) : 0.5496371 object centre at (A) : -35.32350 -2.590001 3.251001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5474398E-02 1.8887594E-02 midg,1,midg; midg,igrid,midg 1.3844253E-02 1.8694378E-02 1,midg,midg; igrid,midg,midg 4.9475473E-03 2.8735595E-03 gauss-seidel spectral radius is 0.9983942 estimated iterations to convergence 198 setup time was (sec) 1.100000 now iterating at: 16:19:57 rms-change max change #iterations 4.441027 160.9921 at 10iterations 1.952386 67.87219 at 20iterations 0.8578582 26.47418 at 30iterations 0.3776260 11.29241 at 40iterations 0.1661172 4.717392 at 50iterations 7.3204309E-02 2.163921 at 60iterations 3.2442328E-02 1.077432 at 70iterations 1.4449700E-02 0.4328051 at 80iterations 6.5737348E-03 0.2019119 at 90iterations 3.1728130E-03 9.8545074E-02 at 100iterations 1.6814638E-03 5.3998947E-02 at 110iterations 1.0267865E-03 2.8884888E-02 at 120iterations finished qdiffx linear iterations at : 16:20:05 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 1.0267865E-03 2.8884888E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.840000 DelPhi exited at 16:20:05 8.841u 0.219s 0:09.33 96.9% 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 16:20:05 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 = 4811 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.473367 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): -63.08800 -7.559000 ymin,ymax (A): -34.81000 29.63000 zmin,zma (A): -29.13400 35.63600 x,y,z range (A): 55.52900 64.44000 64.77000 scale (grids/A): 2.473367 object centre (A): -35.32350 -2.590001 3.251001 number of atom coordinates read : 4811 total number of charged atoms : 4653 net assigned charge : 7.000030 assigned positive charge : 724.2505 centred at (gu) : 92.39211 89.77971 83.42690 assigned negative charge : -717.2551 centred at (gu) : 92.42644 89.93903 83.44707 start vw surface at 0.2500000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 242967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39165 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 116001 mr = 181661 m= 33910 mr = 92929 m= 5838 mr = 25974 m= 487 mr = 3974 m= 11 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 6004 time to turn everything in is 1.880000 number of dielectric boundary points 94415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 37182 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) : 1.648911 object centre at (A) : -35.32350 -2.590001 3.251001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4577121 0.5654881 midg,1,midg; midg,igrid,midg 0.1411645 0.4336445 1,midg,midg; igrid,midg,midg 9.0967134E-02 6.1665200E-02 gauss-seidel spectral radius is 0.9992412 estimated iterations to convergence 287 setup time was (sec) 2.210000 now iterating at: 16:20:08 rms-change max change #iterations 11.52631 303.8912 at 10iterations 6.803484 162.1355 at 20iterations 3.989000 80.32845 at 30iterations 2.326190 46.58253 at 40iterations 1.349190 24.33511 at 50iterations 0.7815754 15.03263 at 60iterations 0.4519932 8.364534 at 70iterations 0.2609617 4.930325 at 80iterations 0.1503678 2.503845 at 90iterations 8.6522408E-02 1.467205 at 100iterations 4.9774516E-02 0.9364929 at 110iterations 2.8639315E-02 0.5205231 at 120iterations 1.6501041E-02 0.3245907 at 130iterations 9.5431637E-03 0.1610903 at 140iterations 5.5828406E-03 9.1468811E-02 at 150iterations 3.3261622E-03 5.4046631E-02 at 160iterations 2.0515400E-03 3.8206100E-02 at 170iterations 1.3395397E-03 2.3994446E-02 at 180iterations finished qdiffx linear iterations at : 16:20:19 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 1.3395397E-03 2.3994446E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 16:20:20 13.744u 0.206s 0:14.25 97.8% 0+0k 0+0io 0pf+0w