Tue Oct 11 06:46:20 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 06:46:20 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 = 3505 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5779127 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): -23.81800 34.24000 ymin,ymax (A): -42.63800 18.96300 zmin,zma (A): 37.07000 87.16700 x,y,z range (A): 58.05800 61.60100 50.09700 scale (grids/A): 0.5779127 object centre (A): 5.211001 -11.83750 62.11850 number of atom coordinates read : 3505 total number of charged atoms : 3371 net assigned charge : -6.999971 assigned positive charge : 524.4085 centred at (gu) : 87.30184 89.63560 90.32576 assigned negative charge : -531.4097 centred at (gu) : 87.33145 89.87156 90.20499 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7832 nv = 96 ne = 84 npr = 69472 no. pairs analyzed = 69472 no. exposed pairs = 4747 no. arc points = 32879 no. surface atoms = 1581 nbur = 1924 mkacc time = 0.1100000 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 = 1.484000 m= 347 mr = 3943 m= 0 mr = 11 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3298 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1114725E-09 1.5640911E-09 midg,1,midg; midg,igrid,midg 4.5109716E-09 -6.7564225E-09 1,midg,midg; igrid,midg,midg -1.3350254E-09 -1.1784921E-09 gauss-seidel spectral radius is 0.9845968 estimated iterations to convergence 66 setup time was (sec) 0.4200000 now iterating at: 06:46:21 rms-change max change #iterations 0.1058872 17.67178 at 10iterations 8.4519573E-03 1.123680 at 20iterations 9.4749749E-04 0.1261864 at 30iterations 2.2495125E-04 2.3300171E-02 at 40iterations 6.9633068E-05 7.1716309E-03 at 50iterations finished qdiffx linear iterations at : 06:46:24 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 6.9633068E-05 7.1716309E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 06:46:24 3.463u 0.198s 0:04.13 88.3% 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 Tue Oct 11 2011 at 06:46:24 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 = 3505 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.733738 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): -23.81800 34.24000 ymin,ymax (A): -42.63800 18.96300 zmin,zma (A): 37.07000 87.16700 x,y,z range (A): 58.05800 61.60100 50.09700 scale (grids/A): 1.733738 object centre (A): 5.211001 -11.83750 62.11850 number of atom coordinates read : 3505 total number of charged atoms : 3371 net assigned charge : -6.999971 assigned positive charge : 524.4085 centred at (gu) : 81.90443 88.90558 90.97662 assigned negative charge : -531.4097 centred at (gu) : 81.99393 89.61424 90.61441 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 85171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32879 grid for indexing accessible points = 1.400000 m= 27359 mr = 56783 m= 3017 mr = 18408 m= 94 mr = 1407 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 39040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 309 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 26207 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) : 0.5779127 object centre at (A) : 5.211001 -11.83750 62.11850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3139891E-02 1.2107413E-02 midg,1,midg; midg,igrid,midg 5.0515957E-02 -2.5867155E-02 1,midg,midg; igrid,midg,midg -1.7940382E-02 -1.0972407E-02 gauss-seidel spectral radius is 0.9984569 estimated iterations to convergence 202 setup time was (sec) 0.6500000 now iterating at: 06:46:25 rms-change max change #iterations 4.156633 165.7941 at 10iterations 1.850729 74.95471 at 20iterations 0.8235077 26.80431 at 30iterations 0.3674477 11.14707 at 40iterations 0.1641794 5.496904 at 50iterations 7.3622167E-02 2.463046 at 60iterations 3.2904673E-02 1.101812 at 70iterations 1.4688183E-02 0.4557800 at 80iterations 6.5920926E-03 0.2088509 at 90iterations 2.9794432E-03 0.1083865 at 100iterations 1.3628821E-03 4.5151711E-02 at 110iterations 6.3145621E-04 1.8355370E-02 at 120iterations finished qdiffx linear iterations at : 06:46:33 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 6.3145621E-04 1.8355370E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 06:46:33 8.027u 0.200s 0:08.57 95.9% 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 Tue Oct 11 2011 at 06:46:33 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 = 3505 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.600607 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): -23.81800 34.24000 ymin,ymax (A): -42.63800 18.96300 zmin,zma (A): 37.07000 87.16700 x,y,z range (A): 58.05800 61.60100 50.09700 scale (grids/A): 2.600607 object centre (A): 5.211001 -11.83750 62.11850 number of atom coordinates read : 3505 total number of charged atoms : 3371 net assigned charge : -6.999971 assigned positive charge : 524.4085 centred at (gu) : 77.85660 88.35822 91.46481 assigned negative charge : -531.4097 centred at (gu) : 77.99078 89.42127 90.92131 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 197522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32879 grid for indexing accessible points = 1.400000 m= 92984 mr = 139103 m= 27821 mr = 72643 m= 4748 mr = 20425 m= 399 mr = 3038 m= 13 mr = 167 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 88112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 26946 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) : 1.733738 object centre at (A) : 5.211001 -11.83750 62.11850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1741277 0.1699436 midg,1,midg; midg,igrid,midg 0.8705947 -0.1221578 1,midg,midg; igrid,midg,midg -0.2429899 -0.1294121 gauss-seidel spectral radius is 0.9992437 estimated iterations to convergence 287 setup time was (sec) 1.270000 now iterating at: 06:46:35 rms-change max change #iterations 10.52343 282.8920 at 10iterations 6.259118 146.4976 at 20iterations 3.677862 86.72914 at 30iterations 2.150612 47.04301 at 40iterations 1.250379 25.71032 at 50iterations 0.7247738 14.63582 at 60iterations 0.4188661 8.850986 at 70iterations 0.2415303 4.481140 at 80iterations 0.1393583 2.720657 at 90iterations 8.0066077E-02 1.576805 at 100iterations 4.5950394E-02 0.8223414 at 110iterations 2.6414374E-02 0.4603977 at 120iterations 1.5135421E-02 0.2847977 at 130iterations 8.6831674E-03 0.1538811 at 140iterations 4.9777459E-03 0.1058769 at 150iterations 2.8555882E-03 5.8685303E-02 at 160iterations 1.6453712E-03 3.0635357E-02 at 170iterations 9.4754528E-04 1.8070221E-02 at 180iterations finished qdiffx linear iterations at : 06:46:46 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 9.4754528E-04 1.8070221E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 06:46:47 12.907u 0.214s 0:13.41 97.7% 0+0k 0+0io 0pf+0w