Mon Oct 10 14:37:38 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 Mon Oct 10 2011 at 14:37:38 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7397096 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): -20.67200 24.28200 ymin,ymax (A): -7.896000 35.84200 zmin,zma (A): -3.473000 44.65400 x,y,z range (A): 44.95400 43.73800 48.12700 scale (grids/A): 0.7397096 object centre (A): 1.805000 13.97300 20.59050 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 88.91945 90.53684 90.06795 assigned negative charge : -324.4520 centred at (gu) : 88.96105 90.61347 90.22807 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7890 nv = 96 ne = 84 npr = 43663 no. pairs analyzed = 43663 no. exposed pairs = 2716 no. arc points = 19060 no. surface atoms = 925 nbur = 1190 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 525 mr = 4352 m= 5 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.1800000 number of dielectric boundary points 3973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1546 ## 115 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8358 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5738482E-08 -2.7448547E-07 midg,1,midg; midg,igrid,midg -2.4886605E-08 -2.0293839E-07 1,midg,midg; igrid,midg,midg -7.5145316E-08 -1.2105248E-07 gauss-seidel spectral radius is 0.9904764 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 14:37:39 rms-change max change #iterations 0.2493806 33.44634 at 10iterations 3.3300053E-02 4.555356 at 20iterations 4.4184746E-03 0.6610527 at 30iterations 6.0271559E-04 7.1161270E-02 at 40iterations 8.1217389E-05 1.1268616E-02 at 50iterations finished qdiffx linear iterations at : 14:37:42 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 8.1217389E-05 1.1268616E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 14:37:42 3.316u 0.159s 0:03.76 92.0% 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 Mon Oct 10 2011 at 14:37:42 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.219129 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): -20.67200 24.28200 ymin,ymax (A): -7.896000 35.84200 zmin,zma (A): -3.473000 44.65400 x,y,z range (A): 44.95400 43.73800 48.12700 scale (grids/A): 2.219129 object centre (A): 1.805000 13.97300 20.59050 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 86.75806 91.61057 90.20386 assigned negative charge : -324.4520 centred at (gu) : 86.88323 91.84057 90.68401 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19060 grid for indexing accessible points = 1.400000 m= 32774 mr = 57275 m= 7053 mr = 24794 m= 840 mr = 4898 m= 32 mr = 471 m= 0 mr = 9 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1633 time to turn everything in is 0.4100000 number of dielectric boundary points 36516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15736 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) : 0.7397096 object centre at (A) : 1.805000 13.97300 20.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2349199E-02 -0.1337548 midg,1,midg; midg,igrid,midg -2.3089141E-02 -3.2004531E-02 1,midg,midg; igrid,midg,midg -1.1853172E-02 -8.1439205E-03 gauss-seidel spectral radius is 0.9989257 estimated iterations to convergence 241 setup time was (sec) 0.6300000 now iterating at: 14:37:43 rms-change max change #iterations 5.110605 194.5913 at 10iterations 2.583199 80.42952 at 20iterations 1.318177 37.36118 at 30iterations 0.6732007 20.03799 at 40iterations 0.3415372 9.490095 at 50iterations 0.1743307 5.313219 at 60iterations 8.8931158E-02 2.743313 at 70iterations 4.5155596E-02 1.245274 at 80iterations 2.3032859E-02 0.6218987 at 90iterations 1.1744883E-02 0.3383293 at 100iterations 5.9894985E-03 0.1543667 at 110iterations 3.0488037E-03 8.2691193E-02 at 120iterations finished qdiffx linear iterations at : 14:37:50 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 3.0488037E-03 8.2691193E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:37:50 7.783u 0.184s 0:08.24 96.6% 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 Mon Oct 10 2011 at 14:37:50 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.328693 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): -20.67200 24.28200 ymin,ymax (A): -7.896000 35.84200 zmin,zma (A): -3.473000 44.65400 x,y,z range (A): 44.95400 43.73800 48.12700 scale (grids/A): 3.328693 object centre (A): 1.805000 13.97300 20.59050 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 85.13702 92.41572 90.30576 assigned negative charge : -324.4520 centred at (gu) : 85.32481 92.76092 91.02596 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 191791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19060 grid for indexing accessible points = 1.400000 m= 100757 mr = 138366 m= 42664 mr = 83102 m= 13703 mr = 35306 m= 3307 mr = 10880 m= 493 mr = 2550 m= 39 mr = 340 m= 0 mr = 12 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 5823 time to turn everything in is 1.280000 number of dielectric boundary points 82198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 15808 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) : 2.219129 object centre at (A) : 1.805000 13.97300 20.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3370161E-02 -1.276145 midg,1,midg; midg,igrid,midg -0.2121774 -0.1896493 1,midg,midg; igrid,midg,midg -0.2243183 -0.1023296 gauss-seidel spectral radius is 0.9993172 estimated iterations to convergence 302 setup time was (sec) 1.510000 now iterating at: 14:37:52 rms-change max change #iterations 11.00443 337.4178 at 10iterations 6.477272 126.5692 at 20iterations 3.814275 64.58211 at 30iterations 2.241553 38.37868 at 40iterations 1.319141 21.95528 at 50iterations 0.7743890 13.11946 at 60iterations 0.4552327 7.385092 at 70iterations 0.2670697 4.878534 at 80iterations 0.1569144 2.602708 at 90iterations 9.2091128E-02 1.513505 at 100iterations 5.3941119E-02 0.8317108 at 110iterations 3.1621527E-02 0.5604548 at 120iterations 1.8583097E-02 0.3010931 at 130iterations 1.0911445E-02 0.1669693 at 140iterations 6.3997428E-03 0.1008918 at 150iterations 3.7499622E-03 5.8740616E-02 at 160iterations 2.2065749E-03 3.9165020E-02 at 170iterations 1.2902941E-03 2.1018982E-02 at 180iterations finished qdiffx linear iterations at : 14:38:03 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.2902941E-03 2.1018982E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 14:38:04 12.944u 0.201s 0:13.77 95.4% 0+0k 0+0io 0pf+0w