Wed Feb 15 08:55:58 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:58 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4236 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5408115 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 0.5408115 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4236 total number of charged atoms : 4087 net assigned charge : 2.000051 assigned positive charge : 627.1864 centred at (gu) : 90.25095 92.18813 90.13595 assigned negative charge : -625.1909 centred at (gu) : 90.31511 92.23761 90.10125 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7888 nv = 96 ne = 84 npr = 87323 no. pairs analyzed = 87323 no. exposed pairs = 5325 no. arc points = 37226 no. surface atoms = 1822 nbur = 2414 mkacc time = 0.1500000 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= 348 mr = 4074 m= 0 mr = 17 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3699 ## 446 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10550 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4956636E-10 3.8832015E-10 midg,1,midg; midg,igrid,midg 2.8296279E-10 -4.7757742E-10 1,midg,midg; igrid,midg,midg 5.6102267E-10 -4.0847947E-10 gauss-seidel spectral radius is 0.9824730 estimated iterations to convergence 62 setup time was (sec) 0.5000000 now iterating at: 08:55:59 rms-change max change #iterations 8.2364552E-02 11.97062 at 10iterations 5.5569410E-03 0.8515356 at 20iterations 5.3300819E-04 8.0207825E-02 at 30iterations 1.4565696E-04 2.2513866E-02 at 40iterations 5.1495666E-05 7.8668594E-03 at 50iterations finished qdiffx linear iterations at : 08:56:02 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 5.1495666E-05 7.8668594E-03 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 08:56:05 3.778u 0.238s 0:06.87 58.2% 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 Wed Feb 15 2012 at 08:56:05 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4236 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.622435 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 1.622435 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4236 total number of charged atoms : 4087 net assigned charge : 2.000051 assigned positive charge : 627.1864 centred at (gu) : 90.75150 96.56245 90.40638 assigned negative charge : -625.1909 centred at (gu) : 90.94509 96.71249 90.30373 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 87601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37226 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 27467 mr = 59287 m= 2894 mr = 18804 m= 76 mr = 1397 m= 0 mr = 5 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 518 time to turn everything in is 0.4500000 number of dielectric boundary points 38545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 371 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 31298 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) : 0.5408115 object centre at (A) : 25.34350 50.68350 13.35450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2993156E-02 2.2057192E-03 midg,1,midg; midg,igrid,midg 9.9606961E-03 -3.3165365E-03 1,midg,midg; igrid,midg,midg -2.0326502E-03 -1.1105921E-02 gauss-seidel spectral radius is 0.9982982 estimated iterations to convergence 192 setup time was (sec) 0.6700000 now iterating at: 08:56:06 rms-change max change #iterations 4.033942 194.5952 at 10iterations 1.725986 64.42272 at 20iterations 0.7415057 22.86701 at 30iterations 0.3175205 11.12852 at 40iterations 0.1366088 5.263434 at 50iterations 5.8657154E-02 1.758586 at 60iterations 2.5184050E-02 0.7845287 at 70iterations 1.0808711E-02 0.3643665 at 80iterations 4.6730554E-03 0.1474838 at 90iterations 2.0345415E-03 6.1691284E-02 at 100iterations 8.9808129E-04 2.9283524E-02 at 110iterations 4.1400664E-04 1.4760971E-02 at 120iterations finished qdiffx linear iterations at : 08:56:14 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 4.1400664E-04 1.4760971E-02 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.590000 DelPhi exited at 08:56:14 8.595u 0.208s 0:09.17 95.8% 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 Wed Feb 15 2012 at 08:56:15 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4236 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.433652 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 2.433652 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4236 total number of charged atoms : 4087 net assigned charge : 2.000051 assigned positive charge : 627.1864 centred at (gu) : 91.12696 99.84318 90.60916 assigned negative charge : -625.1909 centred at (gu) : 91.41762 100.0688 90.45526 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 203808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37226 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 94157 mr = 145705 m= 27578 mr = 73923 m= 4387 mr = 20684 m= 265 mr = 2848 m= 2 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1645 time to turn everything in is 1.080000 number of dielectric boundary points 86938 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 32668 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) : 1.622435 object centre at (A) : 25.34350 50.68350 13.35450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1095914 -5.5955254E-02 midg,1,midg; midg,igrid,midg 0.1004072 -0.1389067 1,midg,midg; igrid,midg,midg -7.6107875E-02 -3.6940850E-02 gauss-seidel spectral radius is 0.9992077 estimated iterations to convergence 280 setup time was (sec) 1.330000 now iterating at: 08:56:16 rms-change max change #iterations 10.46251 509.3339 at 10iterations 6.077700 163.9796 at 20iterations 3.506443 82.23167 at 30iterations 2.014140 40.79421 at 40iterations 1.152296 24.48468 at 50iterations 0.6557046 12.88145 at 60iterations 0.3728282 6.560440 at 70iterations 0.2118622 3.909912 at 80iterations 0.1199167 2.237426 at 90iterations 6.7842543E-02 1.175102 at 100iterations 3.8470574E-02 0.7080231 at 110iterations 2.1763753E-02 0.3998299 at 120iterations 1.2296233E-02 0.2132263 at 130iterations 6.9502401E-03 0.1323395 at 140iterations 3.9308574E-03 7.2193146E-02 at 150iterations 2.2316037E-03 4.5066833E-02 at 160iterations 1.2715864E-03 2.3815155E-02 at 170iterations 7.3000125E-04 1.3321877E-02 at 180iterations finished qdiffx linear iterations at : 08:56:28 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 7.3000125E-04 1.3321877E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 08:56:29 13.221u 0.235s 0:14.26 94.3% 0+0k 0+0io 0pf+0w