Tue Oct 11 03:26:27 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 03:26:27 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 = 2665 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: 0.5978873 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): -18.70700 33.49700 ymin,ymax (A): 37.80000 97.34300 zmin,zma (A): -12.60900 40.42800 x,y,z range (A): 52.20399 59.54300 53.03700 scale (grids/A): 0.5978873 object centre (A): 7.395000 67.57150 13.90950 number of atom coordinates read : 2665 total number of charged atoms : 2520 net assigned charge : 6.500027 assigned positive charge : 405.4018 centred at (gu) : 92.69522 92.43784 89.16228 assigned negative charge : -398.9026 centred at (gu) : 92.71882 92.40836 89.16956 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6244 nv = 96 ne = 84 npr = 53366 no. pairs analyzed = 53366 no. exposed pairs = 3387 no. arc points = 24312 no. surface atoms = 1144 nbur = 1521 mkacc time = 8.9999996E-02 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 = 1.456000 m= 267 mr = 3236 m= 1 mr = 21 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 0.2000000 number of dielectric boundary points 3255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2471 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7883 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3749050E-09 1.9158695E-09 midg,1,midg; midg,igrid,midg 9.1794894E-10 6.1961862E-09 1,midg,midg; igrid,midg,midg 1.8618734E-09 3.1177225E-09 gauss-seidel spectral radius is 0.9855283 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 03:26:27 rms-change max change #iterations 0.1060577 19.51138 at 10iterations 8.8208038E-03 1.271590 at 20iterations 7.2732376E-04 0.1085336 at 30iterations 6.3326224E-05 1.0061741E-02 at 40iterations 5.3051344E-06 7.6770782E-04 at 50iterations finished qdiffx linear iterations at : 03:26:30 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 5.3051344E-06 7.6770782E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 03:26:30 3.352u 0.179s 0:03.84 91.6% 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 03:26:30 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 = 2665 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: 1.793662 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): -18.70700 33.49700 ymin,ymax (A): 37.80000 97.34300 zmin,zma (A): -12.60900 40.42800 x,y,z range (A): 52.20399 59.54300 53.03700 scale (grids/A): 1.793662 object centre (A): 7.395000 67.57150 13.90950 number of atom coordinates read : 2665 total number of charged atoms : 2520 net assigned charge : 6.500027 assigned positive charge : 405.4018 centred at (gu) : 98.08513 97.31297 87.48631 assigned negative charge : -398.9026 centred at (gu) : 98.15630 97.22501 87.50864 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24312 grid for indexing accessible points = 1.400000 m= 22483 mr = 46406 m= 2676 mr = 15896 m= 84 mr = 1489 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 427 time to turn everything in is 0.3300000 number of dielectric boundary points 29964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19699 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) : 0.5978873 object centre at (A) : 7.395000 67.57150 13.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9308176E-02 4.0140147E-03 midg,1,midg; midg,igrid,midg -1.0170839E-02 1.1084802E-02 1,midg,midg; igrid,midg,midg -3.0042727E-03 7.9000732E-03 gauss-seidel spectral radius is 0.9984640 estimated iterations to convergence 202 setup time was (sec) 0.5400000 now iterating at: 03:26:31 rms-change max change #iterations 3.794252 166.1152 at 10iterations 1.700642 72.52367 at 20iterations 0.7628940 26.07822 at 30iterations 0.3417726 12.17640 at 40iterations 0.1531388 6.146147 at 50iterations 6.8658113E-02 2.601063 at 60iterations 3.0646164E-02 1.234851 at 70iterations 1.3791873E-02 0.4815397 at 80iterations 6.1470061E-03 0.2174492 at 90iterations 2.7547586E-03 9.1724873E-02 at 100iterations 1.2362346E-03 4.2131424E-02 at 110iterations 5.5121112E-04 1.8783569E-02 at 120iterations finished qdiffx linear iterations at : 03:26:38 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 5.5121112E-04 1.8783569E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 03:26:39 7.628u 0.203s 0:08.23 95.0% 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 03:26:39 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 = 2665 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: 2.690493 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): -18.70700 33.49700 ymin,ymax (A): 37.80000 97.34300 zmin,zma (A): -12.60900 40.42800 x,y,z range (A): 52.20399 59.54300 53.03700 scale (grids/A): 2.690493 object centre (A): 7.395000 67.57150 13.90950 number of atom coordinates read : 2665 total number of charged atoms : 2520 net assigned charge : 6.500027 assigned positive charge : 405.4018 centred at (gu) : 102.1274 100.9693 86.22932 assigned negative charge : -398.9026 centred at (gu) : 102.2343 100.8373 86.26284 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 158854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24312 grid for indexing accessible points = 1.400000 m= 75600 mr = 113094 m= 23655 mr = 60740 m= 4473 mr = 18260 m= 407 mr = 3141 m= 7 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1201 time to turn everything in is 0.8300000 number of dielectric boundary points 67534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20155 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) : 1.793662 object centre at (A) : 7.395000 67.57150 13.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1541310 -5.8590885E-02 midg,1,midg; midg,igrid,midg -0.1091276 5.6644820E-02 1,midg,midg; igrid,midg,midg -9.8370388E-02 0.1392630 gauss-seidel spectral radius is 0.9992175 estimated iterations to convergence 282 setup time was (sec) 1.060000 now iterating at: 03:26:40 rms-change max change #iterations 9.192917 300.4222 at 10iterations 5.308520 127.4818 at 20iterations 3.037429 69.43233 at 30iterations 1.736645 39.70753 at 40iterations 0.9894682 23.17216 at 50iterations 0.5619862 11.14920 at 60iterations 0.3198525 7.978626 at 70iterations 0.1819134 3.744350 at 80iterations 0.1029387 2.016129 at 90iterations 5.8329381E-02 1.274470 at 100iterations 3.3049349E-02 0.6922112 at 110iterations 1.8769221E-02 0.3613157 at 120iterations 1.0625652E-02 0.2449188 at 130iterations 6.0222894E-03 0.1301079 at 140iterations 3.4052078E-03 6.4259529E-02 at 150iterations 1.9288338E-03 3.7437916E-02 at 160iterations 1.0908294E-03 2.1635294E-02 at 170iterations 6.1726221E-04 1.1899948E-02 at 180iterations finished qdiffx linear iterations at : 03:26:51 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 6.1726221E-04 1.1899948E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 03:26:52 12.263u 0.211s 0:12.79 97.4% 0+0k 0+0io 0pf+0w