Mon Oct 10 23:38:31 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 23:38:31 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 = 2607 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5914603 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): 10.51400 64.98100 ymin,ymax (A): -3.900000 56.29000 zmin,zma (A): 10.59500 54.06100 x,y,z range (A): 54.46700 60.19000 43.46600 scale (grids/A): 0.5914603 object centre (A): 37.74750 26.19500 32.32800 number of atom coordinates read : 2607 total number of charged atoms : 2466 net assigned charge : 8.000021 assigned positive charge : 391.1287 centred at (gu) : 88.73341 92.35264 89.49814 assigned negative charge : -383.1294 centred at (gu) : 88.70454 92.10301 89.64735 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5971 nv = 96 ne = 84 npr = 52580 no. pairs analyzed = 52580 no. exposed pairs = 3156 no. arc points = 22275 no. surface atoms = 1070 nbur = 1537 mkacc time = 0.1200000 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 = 1.456000 m= 249 mr = 3257 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3400000 number of dielectric boundary points 2940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2154 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7487 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1759905E-09 -1.5588626E-09 midg,1,midg; midg,igrid,midg -2.6540732E-09 1.5632976E-08 1,midg,midg; igrid,midg,midg 2.0945734E-09 2.3904272E-09 gauss-seidel spectral radius is 0.9852065 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 23:38:32 rms-change max change #iterations 0.1003743 14.77284 at 10iterations 9.9085057E-03 1.548210 at 20iterations 1.5572705E-03 0.3569984 at 30iterations 4.2477419E-04 0.1082420 at 40iterations 1.2775543E-04 3.2958984E-02 at 50iterations finished qdiffx linear iterations at : 23:38:35 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.2775543E-04 3.2958984E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 23:38:36 3.506u 0.189s 0:04.42 83.2% 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 23:38:36 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 = 2607 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.774381 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): 10.51400 64.98100 ymin,ymax (A): -3.900000 56.29000 zmin,zma (A): 10.59500 54.06100 x,y,z range (A): 54.46700 60.19000 43.46600 scale (grids/A): 1.774381 object centre (A): 37.74750 26.19500 32.32800 number of atom coordinates read : 2607 total number of charged atoms : 2466 net assigned charge : 8.000021 assigned positive charge : 391.1287 centred at (gu) : 86.19946 97.05758 88.49371 assigned negative charge : -383.1294 centred at (gu) : 86.11339 96.30878 88.94171 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 65336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22275 grid for indexing accessible points = 1.400000 m= 22446 mr = 45404 m= 3012 mr = 16593 m= 105 mr = 1779 m= 0 mr = 15 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 872 time to turn everything in is 0.5600000 number of dielectric boundary points 27108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19197 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) : 0.5914603 object centre at (A) : 37.74750 26.19500 32.32800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2560827E-02 3.1338199E-03 midg,1,midg; midg,igrid,midg -1.1728676E-02 2.3922570E-02 1,midg,midg; igrid,midg,midg -4.4276663E-03 1.3959102E-02 gauss-seidel spectral radius is 0.9984254 estimated iterations to convergence 200 setup time was (sec) 0.8700000 now iterating at: 23:38:37 rms-change max change #iterations 3.666089 172.7635 at 10iterations 1.614694 62.74825 at 20iterations 0.7165551 27.60062 at 30iterations 0.3182237 11.37386 at 40iterations 0.1411848 4.608585 at 50iterations 6.3217312E-02 2.235399 at 60iterations 2.8061081E-02 0.9504700 at 70iterations 1.2614616E-02 0.4361572 at 80iterations 5.7614921E-03 0.2172279 at 90iterations 2.7386965E-03 0.1066666 at 100iterations 1.3625835E-03 5.5534363E-02 at 110iterations 7.1567454E-04 3.2070160E-02 at 120iterations finished qdiffx linear iterations at : 23:38:44 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 7.1567454E-04 3.2070160E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 23:38:45 7.799u 0.239s 0:08.75 91.6% 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 23:38:45 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 = 2607 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: 2.661572 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): 10.51400 64.98100 ymin,ymax (A): -3.900000 56.29000 zmin,zma (A): 10.59500 54.06100 x,y,z range (A): 54.46700 60.19000 43.46600 scale (grids/A): 2.661572 object centre (A): 37.74750 26.19500 32.32800 number of atom coordinates read : 2607 total number of charged atoms : 2466 net assigned charge : 8.000021 assigned positive charge : 391.1287 centred at (gu) : 84.29923 100.5862 87.74030 assigned negative charge : -383.1294 centred at (gu) : 84.17003 99.46320 88.41245 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 151246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22275 grid for indexing accessible points = 1.400000 m= 74502 mr = 110164 m= 25024 mr = 60999 m= 5091 mr = 20045 m= 447 mr = 3788 m= 13 mr = 226 m= 0 mr = 1 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 3103 time to turn everything in is 1.170000 number of dielectric boundary points 61100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 19725 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) : 1.774381 object centre at (A) : 37.74750 26.19500 32.32800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2678194 5.0157633E-02 midg,1,midg; midg,igrid,midg -0.2412620 -0.1323330 1,midg,midg; igrid,midg,midg -9.5018864E-02 0.1109498 gauss-seidel spectral radius is 0.9991958 estimated iterations to convergence 278 setup time was (sec) 1.490000 now iterating at: 23:38:46 rms-change max change #iterations 8.904963 305.3685 at 10iterations 5.045870 152.6388 at 20iterations 2.852437 66.34323 at 30iterations 1.614353 37.02979 at 40iterations 0.9077371 17.46099 at 50iterations 0.5124885 10.57527 at 60iterations 0.2883703 6.520470 at 70iterations 0.1620496 3.307553 at 80iterations 9.1171958E-02 1.798038 at 90iterations 5.1291563E-02 0.9749641 at 100iterations 2.8916286E-02 0.5830078 at 110iterations 1.6317273E-02 0.3530121 at 120iterations 9.2656771E-03 0.2127571 at 130iterations 5.3220484E-03 0.1180868 at 140iterations 3.1120565E-03 7.2826385E-02 at 150iterations 1.8704082E-03 4.4765472E-02 at 160iterations 1.1753374E-03 3.0563354E-02 at 170iterations 7.7039748E-04 1.9371033E-02 at 180iterations finished qdiffx linear iterations at : 23:38:56 total time elapsed so far: 11.48000 # loops : 180 mean,max change (kT/e) : 7.7039748E-04 1.9371033E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 23:38:57 11.693u 0.236s 0:12.36 96.4% 0+0k 0+0io 0pf+0w