Mon Oct 10 16:24:07 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 Mon Oct 10 2011 at 16:24:07 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 = 2534 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: 0.5673034 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): 61.47600 112.7820 ymin,ymax (A): 225.3390 288.0920 zmin,zma (A): 84.92900 127.1350 x,y,z range (A): 51.30600 62.75302 42.20600 scale (grids/A): 0.5673034 object centre (A): 87.12900 256.7155 106.0320 number of atom coordinates read : 2534 total number of charged atoms : 2391 net assigned charge : 6.500026 assigned positive charge : 381.4666 centred at (gu) : 90.35797 90.03683 90.41924 assigned negative charge : -374.9674 centred at (gu) : 90.22925 89.88269 90.53044 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5145 nv = 96 ne = 84 npr = 49996 no. pairs analyzed = 49996 no. exposed pairs = 3612 no. arc points = 25800 no. surface atoms = 1203 nbur = 1331 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 = 1.512000 m= 274 mr = 2308 m= 0 mr = 15 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 3096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2562 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6744 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0213045E-09 -5.0855992E-10 midg,1,midg; midg,igrid,midg -9.8118780E-10 2.7598475E-09 1,midg,midg; igrid,midg,midg -6.1292538E-10 2.6569924E-09 gauss-seidel spectral radius is 0.9839369 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 16:24:07 rms-change max change #iterations 8.0548286E-02 14.33159 at 10iterations 5.8767591E-03 1.080322 at 20iterations 4.3331349E-04 8.3209991E-02 at 30iterations 3.4097648E-05 6.2370300E-03 at 40iterations 3.9456768E-06 8.7547302E-04 at 50iterations finished qdiffx linear iterations at : 16:24:10 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 3.9456768E-06 8.7547302E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 16:24:11 3.420u 0.177s 0:03.91 91.8% 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 Mon Oct 10 2011 at 16:24:11 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 = 2534 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: 1.701910 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): 61.47600 112.7820 ymin,ymax (A): 225.3390 288.0920 zmin,zma (A): 84.92900 127.1350 x,y,z range (A): 51.30600 62.75302 42.20600 scale (grids/A): 1.701910 object centre (A): 87.12900 256.7155 106.0320 number of atom coordinates read : 2534 total number of charged atoms : 2391 net assigned charge : 6.500026 assigned positive charge : 381.4666 centred at (gu) : 91.07343 90.11004 91.25696 assigned negative charge : -374.9674 centred at (gu) : 90.68730 89.64770 91.59106 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 54663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25800 grid for indexing accessible points = 1.400000 m= 17652 mr = 33126 m= 2612 mr = 11639 m= 72 mr = 1417 m= 0 mr = 9 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 28808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 18430 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) : 0.5673034 object centre at (A) : 87.12900 256.7155 106.0320 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5812888E-03 -5.9239194E-03 midg,1,midg; midg,igrid,midg 2.3025351E-03 -3.6523144E-03 1,midg,midg; igrid,midg,midg 4.4820858E-03 1.4608996E-02 gauss-seidel spectral radius is 0.9982944 estimated iterations to convergence 192 setup time was (sec) 0.5100000 now iterating at: 16:24:11 rms-change max change #iterations 3.287637 182.4819 at 10iterations 1.402255 58.21864 at 20iterations 0.6002201 25.96903 at 30iterations 0.2567914 10.25272 at 40iterations 0.1096386 4.539307 at 50iterations 4.6575893E-02 1.795408 at 60iterations 2.0042066E-02 0.7209425 at 70iterations 8.5561872E-03 0.3777847 at 80iterations 3.6665406E-03 0.1422215 at 90iterations 1.5747908E-03 5.8212280E-02 at 100iterations 6.6895282E-04 2.7503967E-02 at 110iterations 2.9010727E-04 1.0732412E-02 at 120iterations finished qdiffx linear iterations at : 16:24:19 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.9010727E-04 1.0732412E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 16:24:19 7.801u 0.212s 0:08.29 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 16:24:19 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 = 2534 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: 2.552865 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): 61.47600 112.7820 ymin,ymax (A): 225.3390 288.0920 zmin,zma (A): 84.92900 127.1350 x,y,z range (A): 51.30600 62.75302 42.20600 scale (grids/A): 2.552865 object centre (A): 87.12900 256.7155 106.0320 number of atom coordinates read : 2534 total number of charged atoms : 2391 net assigned charge : 6.500026 assigned positive charge : 381.4666 centred at (gu) : 91.60975 90.16476 91.88523 assigned negative charge : -374.9674 centred at (gu) : 91.03100 89.47147 92.38641 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 126502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25800 grid for indexing accessible points = 1.400000 m= 56301 mr = 82078 m= 20143 mr = 42230 m= 4337 mr = 15257 m= 368 mr = 2978 m= 9 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 64926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19120 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) : 1.701910 object centre at (A) : 87.12900 256.7155 106.0320 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4544087E-02 -8.9150980E-02 midg,1,midg; midg,igrid,midg 5.8250744E-02 -0.7221953 1,midg,midg; igrid,midg,midg 4.0933695E-02 0.1518997 gauss-seidel spectral radius is 0.9991704 estimated iterations to convergence 274 setup time was (sec) 0.9400000 now iterating at: 16:24:20 rms-change max change #iterations 8.538436 328.9624 at 10iterations 4.875898 141.4082 at 20iterations 2.758836 76.00252 at 30iterations 1.557179 41.70445 at 40iterations 0.8716996 20.67780 at 50iterations 0.4885541 11.63531 at 60iterations 0.2728455 6.218286 at 70iterations 0.1521724 3.492282 at 80iterations 8.4514886E-02 1.854074 at 90iterations 4.7056373E-02 1.034650 at 100iterations 2.6151022E-02 0.5394220 at 110iterations 1.4557992E-02 0.3263645 at 120iterations 8.1050685E-03 0.1702919 at 130iterations 4.4976664E-03 9.3688965E-02 at 140iterations 2.4978686E-03 5.0064087E-02 at 150iterations 1.3880917E-03 3.2606125E-02 at 160iterations 7.6868915E-04 2.0231247E-02 at 170iterations 4.2944192E-04 9.6328259E-03 at 180iterations finished qdiffx linear iterations at : 16:24:31 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 4.2944192E-04 9.6328259E-03 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 16:24:32 12.269u 0.202s 0:12.75 97.7% 0+0k 0+0io 0pf+0w