Tue Oct 11 02:23:18 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 02:23:19 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6666791 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): 20.52000 66.77100 ymin,ymax (A): 14.54800 67.94700 zmin,zma (A): -17.46200 29.79100 x,y,z range (A): 46.25100 53.39900 47.25300 scale (grids/A): 0.6666791 object centre (A): 43.64550 41.24750 6.164500 number of atom coordinates read : 2750 total number of charged atoms : 2626 net assigned charge : 4.000017 assigned positive charge : 424.7494 centred at (gu) : 90.74328 90.27843 90.58107 assigned negative charge : -420.7504 centred at (gu) : 90.61966 90.51660 90.62569 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8155 nv = 96 ne = 84 npr = 57087 no. pairs analyzed = 57087 no. exposed pairs = 3370 no. arc points = 22915 no. surface atoms = 1122 nbur = 1628 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4664 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.3700000 number of dielectric boundary points 3887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2128 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0910180E-08 8.8900731E-10 midg,1,midg; midg,igrid,midg 6.7246063E-08 -5.2831421E-08 1,midg,midg; igrid,midg,midg -1.6635195E-08 5.0480093E-08 gauss-seidel spectral radius is 0.9883478 estimated iterations to convergence 76 setup time was (sec) 0.6500000 now iterating at: 02:23:19 rms-change max change #iterations 0.1834248 25.36469 at 10iterations 2.0420661E-02 2.984474 at 20iterations 3.2567168E-03 0.6071472 at 30iterations 9.6209568E-04 0.2010269 at 40iterations 3.5058148E-04 7.4943542E-02 at 50iterations finished qdiffx linear iterations at : 02:23:23 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 3.5058148E-04 7.4943542E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 02:23:23 4.171u 0.267s 0:04.95 89.4% 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 02:23:24 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.000037 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): 20.52000 66.77100 ymin,ymax (A): 14.54800 67.94700 zmin,zma (A): -17.46200 29.79100 x,y,z range (A): 46.25100 53.39900 47.25300 scale (grids/A): 2.000037 object centre (A): 43.64550 41.24750 6.164500 number of atom coordinates read : 2750 total number of charged atoms : 2626 net assigned charge : 4.000017 assigned positive charge : 424.7494 centred at (gu) : 92.22898 90.83443 91.74262 assigned negative charge : -420.7504 centred at (gu) : 91.85880 91.54948 91.87650 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 87843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22915 grid for indexing accessible points = 1.400000 m= 32790 mr = 62252 m= 5431 mr = 24729 m= 395 mr = 3521 m= 7 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 3224 time to turn everything in is 0.7800000 number of dielectric boundary points 35795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20784 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) : 0.6666791 object centre at (A) : 43.64550 41.24750 6.164500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4144920E-02 -2.5499472E-02 midg,1,midg; midg,igrid,midg 7.6878592E-02 -5.8597293E-02 1,midg,midg; igrid,midg,midg -1.1143327E-02 5.0754353E-02 gauss-seidel spectral radius is 0.9987710 estimated iterations to convergence 226 setup time was (sec) 1.080000 now iterating at: 02:23:25 rms-change max change #iterations 4.856474 248.2253 at 10iterations 2.366635 78.74829 at 20iterations 1.150844 36.07377 at 30iterations 0.5608705 16.50094 at 40iterations 0.2731602 7.774445 at 50iterations 0.1329985 4.264101 at 60iterations 6.5295175E-02 2.072396 at 70iterations 3.1960644E-02 0.9331827 at 80iterations 1.5862394E-02 0.4539604 at 90iterations 8.0421437E-03 0.2358856 at 100iterations 4.2112316E-03 0.1420317 at 110iterations 2.3507690E-03 8.4892273E-02 at 120iterations finished qdiffx linear iterations at : 02:23:33 total time elapsed so far: 9.650000 # loops : 120 mean,max change (kT/e) : 2.3507690E-03 8.4892273E-02 energy calculations done at 9.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.820000 DelPhi exited at 02:23:34 9.825u 0.305s 0:10.80 93.7% 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 Tue Oct 11 2011 at 02:23:34 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.000056 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): 20.52000 66.77100 ymin,ymax (A): 14.54800 67.94700 zmin,zma (A): -17.46200 29.79100 x,y,z range (A): 46.25100 53.39900 47.25300 scale (grids/A): 3.000056 object centre (A): 43.64550 41.24750 6.164500 number of atom coordinates read : 2750 total number of charged atoms : 2626 net assigned charge : 4.000017 assigned positive charge : 424.7494 centred at (gu) : 93.34357 91.25169 92.61383 assigned negative charge : -420.7504 centred at (gu) : 92.78812 92.32408 92.81474 start vw surface at 0.1600000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 202860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22915 grid for indexing accessible points = 1.400000 m= 105052 mr = 150393 m= 39079 mr = 86917 m= 10141 mr = 31996 m= 1724 mr = 7816 m= 131 mr = 1250 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 11091 time to turn everything in is 2.030000 number of dielectric boundary points 80552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 21007 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) : 2.000037 object centre at (A) : 43.64550 41.24750 6.164500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2134113 -0.3202296 midg,1,midg; midg,igrid,midg 1.004534 -0.7169075 1,midg,midg; igrid,midg,midg -0.1338029 0.4054006 gauss-seidel spectral radius is 0.9992931 estimated iterations to convergence 297 setup time was (sec) 2.370000 now iterating at: 02:23:37 rms-change max change #iterations 11.18594 368.6103 at 10iterations 6.582672 128.6030 at 20iterations 3.876251 73.08878 at 30iterations 2.273595 45.67546 at 40iterations 1.332617 29.21506 at 50iterations 0.7800120 15.73738 at 60iterations 0.4564899 7.769409 at 70iterations 0.2661138 5.020092 at 80iterations 0.1560327 2.799820 at 90iterations 9.0840004E-02 1.497940 at 100iterations 5.3196970E-02 1.030991 at 110iterations 3.1248040E-02 0.5699654 at 120iterations 1.8429371E-02 0.4291840 at 130iterations 1.0995536E-02 0.2113876 at 140iterations 6.7186579E-03 0.1405754 at 150iterations 4.2398418E-03 9.4467163E-02 at 160iterations 2.8363324E-03 7.5904846E-02 at 170iterations 2.0208238E-03 4.8049927E-02 at 180iterations finished qdiffx linear iterations at : 02:23:51 total time elapsed so far: 16.76000 # loops : 180 mean,max change (kT/e) : 2.0208238E-03 4.8049927E-02 energy calculations done at 16.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.94000 DelPhi exited at 02:23:52 16.944u 0.322s 0:17.92 96.3% 0+0k 0+0io 0pf+0w