Sat Oct 15 11:06:52 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 Sat Oct 15 2011 at 11:06:52 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 = 4069 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: 0.5702204 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): 17.23400 76.05200 ymin,ymax (A): 25.29400 77.16200 zmin,zma (A): 7.850000 70.28200 x,y,z range (A): 58.81800 51.86800 62.43200 scale (grids/A): 0.5702204 object centre (A): 46.64300 51.22800 39.06600 number of atom coordinates read : 4069 total number of charged atoms : 3924 net assigned charge : -1.499956 assigned positive charge : 605.7094 centred at (gu) : 90.53501 90.37673 90.07304 assigned negative charge : -607.2115 centred at (gu) : 90.48369 90.49712 90.15797 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8709 nv = 96 ne = 84 npr = 84802 no. pairs analyzed = 84802 no. exposed pairs = 4715 no. arc points = 31443 no. surface atoms = 1610 nbur = 2459 mkacc time = 0.2200000 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 = 1.512000 m= 406 mr = 5110 m= 0 mr = 38 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.4300000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3288 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5668588E-09 -2.1166775E-09 midg,1,midg; midg,igrid,midg 2.1384945E-09 -3.1395684E-09 1,midg,midg; igrid,midg,midg -1.1794530E-09 1.0036444E-09 gauss-seidel spectral radius is 0.9842103 estimated iterations to convergence 65 setup time was (sec) 0.7200000 now iterating at: 11:06:53 rms-change max change #iterations 0.1055605 15.22139 at 10iterations 8.4166862E-03 1.192913 at 20iterations 9.7764295E-04 0.1331711 at 30iterations 2.4423620E-04 2.6004791E-02 at 40iterations 7.9029945E-05 7.4882507E-03 at 50iterations finished qdiffx linear iterations at : 11:06:56 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 7.9029945E-05 7.4882507E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 11:06:57 4.285u 0.442s 0:05.26 89.7% 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 Sat Oct 15 2011 at 11:06:57 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 = 4069 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: 1.710661 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): 17.23400 76.05200 ymin,ymax (A): 25.29400 77.16200 zmin,zma (A): 7.850000 70.28200 x,y,z range (A): 58.81800 51.86800 62.43200 scale (grids/A): 1.710661 object centre (A): 46.64300 51.22800 39.06600 number of atom coordinates read : 4069 total number of charged atoms : 3924 net assigned charge : -1.499956 assigned positive charge : 605.7094 centred at (gu) : 91.60361 91.12918 90.21802 assigned negative charge : -607.2115 centred at (gu) : 91.45071 91.49090 90.47355 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 97757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31443 grid for indexing accessible points = 1.400000 m= 34383 mr = 71634 m= 4280 mr = 25478 m= 143 mr = 2525 m= 0 mr = 40 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1924 time to turn everything in is 0.7600000 number of dielectric boundary points 36886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 30390 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) : 0.5702204 object centre at (A) : 46.64300 51.22800 39.06600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2259030E-02 -2.2678554E-02 midg,1,midg; midg,igrid,midg 1.3363538E-02 -3.2502331E-02 1,midg,midg; igrid,midg,midg 1.6162004E-03 1.2618473E-02 gauss-seidel spectral radius is 0.9984555 estimated iterations to convergence 202 setup time was (sec) 1.060000 now iterating at: 11:06:59 rms-change max change #iterations 4.411862 156.1749 at 10iterations 1.961881 64.06851 at 20iterations 0.8785498 23.36438 at 30iterations 0.3928673 11.78313 at 40iterations 0.1762266 4.914195 at 50iterations 7.8663938E-02 2.431988 at 60iterations 3.5334393E-02 1.020743 at 70iterations 1.5855102E-02 0.4522133 at 80iterations 7.1456777E-03 0.2101941 at 90iterations 3.2632465E-03 9.7910404E-02 at 100iterations 1.5265471E-03 4.3665886E-02 at 110iterations 7.4033049E-04 2.2037506E-02 at 120iterations finished qdiffx linear iterations at : 11:07:07 total time elapsed so far: 9.930000 # loops : 120 mean,max change (kT/e) : 7.4033049E-04 2.2037506E-02 energy calculations done at 9.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.11000 DelPhi exited at 11:07:08 10.111u 0.485s 0:10.97 96.5% 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 Sat Oct 15 2011 at 11:07:08 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 = 4069 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.565992 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): 17.23400 76.05200 ymin,ymax (A): 25.29400 77.16200 zmin,zma (A): 7.850000 70.28200 x,y,z range (A): 58.81800 51.86800 62.43200 scale (grids/A): 2.565992 object centre (A): 46.64300 51.22800 39.06600 number of atom coordinates read : 4069 total number of charged atoms : 3924 net assigned charge : -1.499956 assigned positive charge : 605.7094 centred at (gu) : 92.40536 91.69366 90.32656 assigned negative charge : -607.2115 centred at (gu) : 92.17587 92.23621 90.71033 start vw surface at 0.1600000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 226887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31443 grid for indexing accessible points = 1.400000 m= 115798 mr = 173322 m= 37382 mr = 95983 m= 7347 mr = 29851 m= 681 mr = 5400 m= 22 mr = 384 m= 0 mr = 10 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 6423 time to turn everything in is 1.950000 number of dielectric boundary points 83167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 31371 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) : 1.710661 object centre at (A) : 46.64300 51.22800 39.06600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1705451 -0.5628302 midg,1,midg; midg,igrid,midg 0.1920751 -0.4101947 1,midg,midg; igrid,midg,midg 0.1618374 0.1623776 gauss-seidel spectral radius is 0.9992358 estimated iterations to convergence 286 setup time was (sec) 2.290000 now iterating at: 11:07:11 rms-change max change #iterations 10.93822 328.1512 at 10iterations 6.375637 118.8232 at 20iterations 3.683738 77.04488 at 30iterations 2.129454 42.39639 at 40iterations 1.224219 20.01473 at 50iterations 0.7033589 13.79976 at 60iterations 0.4033097 8.007467 at 70iterations 0.2305129 4.038425 at 80iterations 0.1317454 2.180021 at 90iterations 7.5344212E-02 1.274025 at 100iterations 4.3140400E-02 0.8706777 at 110iterations 2.4634482E-02 0.4288130 at 120iterations 1.4107124E-02 0.2805710 at 130iterations 8.1344889E-03 0.1299591 at 140iterations 4.7066491E-03 8.4649444E-02 at 150iterations 2.7615323E-03 5.4977417E-02 at 160iterations 1.6521955E-03 3.0349731E-02 at 170iterations 1.0252132E-03 1.8012047E-02 at 180iterations finished qdiffx linear iterations at : 11:07:26 total time elapsed so far: 17.59000 # loops : 180 mean,max change (kT/e) : 1.0252132E-03 1.8012047E-02 energy calculations done at 17.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.76000 DelPhi exited at 11:07:27 17.769u 0.503s 0:18.85 96.8% 0+0k 0+0io 0pf+0w