Tue Oct 11 03:22:18 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+sph2.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 = amb2.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 03:22:18 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1186 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7502317 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): -6.613000 30.35700 ymin,ymax (A): 1.376000 40.07900 zmin,zma (A): -1.344000 46.10800 x,y,z range (A): 36.97000 38.70300 47.45200 scale (grids/A): 0.7502317 object centre (A): 11.87200 20.72750 22.38200 number of atom coordinates read : 1186 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 89.34737 89.27650 88.43274 assigned negative charge : -172.6512 centred at (gu) : 89.05630 89.27089 88.45803 start vw surface at 5.0000001E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4579 nv = 96 ne = 84 npr = 23122 no. pairs analyzed = 23122 no. exposed pairs = 1532 no. arc points = 11227 no. surface atoms = 516 nbur = 670 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 285 mr = 2370 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 5.0000001E-02 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.1100000 number of dielectric boundary points 2456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 913 ## 96 charges are in solution ## iepsmp to db, and charging done at 0.1700000 number of grid points assigned charge 4586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8461931E-07 7.9934644E-08 midg,1,midg; midg,igrid,midg 1.3460061E-07 1.1066780E-07 1,midg,midg; igrid,midg,midg -9.0260784E-08 2.7673931E-07 gauss-seidel spectral radius is 0.9906458 estimated iterations to convergence 84 setup time was (sec) 0.2900000 now iterating at: 03:22:18 rms-change max change #iterations 0.1917435 39.47546 at 10iterations 2.6194638E-02 4.665854 at 20iterations 3.5570830E-03 0.5544338 at 30iterations 4.8764580E-04 8.4542990E-02 at 40iterations 6.4532360E-05 9.8953247E-03 at 50iterations finished qdiffx linear iterations at : 03:22:21 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 6.4532360E-05 9.8953247E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 03:22:22 3.255u 0.168s 0:03.88 87.8% 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 Tue Oct 11 2011 at 03:22:22 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1186 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.250695 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): -6.613000 30.35700 ymin,ymax (A): 1.376000 40.07900 zmin,zma (A): -1.344000 46.10800 x,y,z range (A): 36.97000 38.70300 47.45200 scale (grids/A): 2.250695 object centre (A): 11.87200 20.72750 22.38200 number of atom coordinates read : 1186 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 88.04232 87.82948 85.29836 assigned negative charge : -172.6512 centred at (gu) : 87.16908 87.81287 85.37426 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 47814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11227 grid for indexing accessible points = 1.400000 m= 17784 mr = 31193 m= 3510 mr = 13212 m= 346 mr = 2350 m= 20 mr = 198 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1429 time to turn everything in is 0.2500000 number of dielectric boundary points 22519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8468 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) : 0.7502317 object centre at (A) : 11.87200 20.72750 22.38200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5448596E-02 5.1532988E-03 midg,1,midg; midg,igrid,midg 4.1349724E-02 3.4556642E-02 1,midg,midg; igrid,midg,midg -2.5119660E-02 4.6074241E-02 gauss-seidel spectral radius is 0.9988646 estimated iterations to convergence 235 setup time was (sec) 0.4700000 now iterating at: 03:22:22 rms-change max change #iterations 3.764234 200.6226 at 10iterations 1.873955 79.05325 at 20iterations 0.9386304 38.05215 at 30iterations 0.4683430 21.19715 at 40iterations 0.2342463 9.331371 at 50iterations 0.1170994 4.842196 at 60iterations 5.8305819E-02 2.108363 at 70iterations 2.9171191E-02 1.010811 at 80iterations 1.4499257E-02 0.5260353 at 90iterations 7.2487765E-03 0.2595901 at 100iterations 3.6232301E-03 0.1335144 at 110iterations 1.8132719E-03 6.4024925E-02 at 120iterations finished qdiffx linear iterations at : 03:22:29 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.8132719E-03 6.4024925E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 03:22:30 7.524u 0.185s 0:08.01 96.1% 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 03:22:30 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1186 !!! WARNING: HIT 60 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.376043 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): -6.613000 30.35700 ymin,ymax (A): 1.376000 40.07900 zmin,zma (A): -1.344000 46.10800 x,y,z range (A): 36.97000 38.70300 47.45200 scale (grids/A): 3.376043 object centre (A): 11.87200 20.72750 22.38200 number of atom coordinates read : 1186 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.1651 centred at (gu) : 87.06354 86.74419 82.94758 assigned negative charge : -172.6512 centred at (gu) : 85.75370 86.71935 83.06147 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 109875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11227 grid for indexing accessible points = 1.400000 m= 55047 mr = 75284 m= 22561 mr = 44824 m= 6641 mr = 18466 m= 1344 mr = 5146 m= 210 mr = 996 m= 25 mr = 145 m= 0 mr = 20 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 4683 time to turn everything in is 0.7600000 number of dielectric boundary points 50822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 8488 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) : 2.250695 object centre at (A) : 11.87200 20.72750 22.38200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3219125 1.1442159E-02 midg,1,midg; midg,igrid,midg 0.3639735 0.2955529 1,midg,midg; igrid,midg,midg -0.1930707 0.3358467 gauss-seidel spectral radius is 0.9992979 estimated iterations to convergence 298 setup time was (sec) 0.9800000 now iterating at: 03:22:31 rms-change max change #iterations 8.089364 293.8070 at 10iterations 4.721488 123.9083 at 20iterations 2.742775 61.22937 at 30iterations 1.591923 37.35229 at 40iterations 0.9252166 20.78061 at 50iterations 0.5367718 10.68096 at 60iterations 0.3112561 6.659099 at 70iterations 0.1806263 3.696865 at 80iterations 0.1047395 2.223980 at 90iterations 6.1205134E-02 1.380478 at 100iterations 3.5357315E-02 0.7355385 at 110iterations 2.0574581E-02 0.4846287 at 120iterations 1.1949879E-02 0.2562866 at 130iterations 6.9524683E-03 0.1385398 at 140iterations 4.0338389E-03 8.2387924E-02 at 150iterations 2.3521157E-03 4.6957016E-02 at 160iterations 1.3622550E-03 2.9373169E-02 at 170iterations 7.9405820E-04 1.7681479E-02 at 180iterations finished qdiffx linear iterations at : 03:22:42 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 7.9405820E-04 1.7681479E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 03:22:42 11.990u 0.201s 0:12.51 97.4% 0+0k 0+0io 0pf+0w