Mon Oct 10 11:04:47 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 11:04:47 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 = 5411 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: 0.4842220 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): 43.84600 117.3660 ymin,ymax (A): -30.01600 38.72500 zmin,zma (A): -32.24100 33.62700 x,y,z range (A): 73.52000 68.74100 65.86800 scale (grids/A): 0.4842220 object centre (A): 80.60600 4.354500 0.6929989 number of atom coordinates read : 5411 total number of charged atoms : 5255 net assigned charge : 10.50003 assigned positive charge : 853.6298 centred at (gu) : 89.71857 90.58818 91.02129 assigned negative charge : -843.1379 centred at (gu) : 89.67270 90.61478 91.05329 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7981 nv = 96 ne = 84 npr = 106413 no. pairs analyzed = 106413 no. exposed pairs = 6553 no. arc points = 45290 no. surface atoms = 2203 nbur = 3208 mkacc time = 0.2800000 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 = 1.764000 m= 244 mr = 4205 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4401 ## 789 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 10843 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5564036E-11 1.7682284E-11 midg,1,midg; midg,igrid,midg 5.8265816E-11 2.1884591E-11 1,midg,midg; igrid,midg,midg 6.0780320E-13 7.9760511E-11 gauss-seidel spectral radius is 0.9782434 estimated iterations to convergence 56 setup time was (sec) 0.8800000 now iterating at: 11:04:48 rms-change max change #iterations 5.4309674E-02 7.775307 at 10iterations 3.0996387E-03 0.4751587 at 20iterations 8.7482401E-04 0.1417055 at 30iterations 4.2360616E-04 7.0603371E-02 at 40iterations 2.0833753E-04 3.5136223E-02 at 50iterations finished qdiffx linear iterations at : 11:04:52 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 2.0833753E-04 3.5136223E-02 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.360000 DelPhi exited at 11:04:53 5.366u 0.467s 0:06.14 94.7% 0+0k 0+0io 6pf+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 11:04:53 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 = 5411 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: 1.452666 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): 43.84600 117.3660 ymin,ymax (A): -30.01600 38.72500 zmin,zma (A): -32.24100 33.62700 x,y,z range (A): 73.52000 68.74100 65.86800 scale (grids/A): 1.452666 object centre (A): 80.60600 4.354500 0.6929989 number of atom coordinates read : 5411 total number of charged atoms : 5255 net assigned charge : 10.50003 assigned positive charge : 853.6298 centred at (gu) : 89.15397 91.76276 93.06187 assigned negative charge : -843.1379 centred at (gu) : 89.01804 91.84435 93.15965 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 92527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 25290 mr = 64996 m= 1747 mr = 16756 m= 18 mr = 588 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 0.7800000 number of dielectric boundary points 37242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 741 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 38670 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) : 0.4842220 object centre at (A) : 80.60600 4.354500 0.6929989 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5405761E-03 -4.2252577E-04 midg,1,midg; midg,igrid,midg 1.3230298E-02 -3.7006815E-03 1,midg,midg; igrid,midg,midg -2.3675429E-02 6.8648476E-03 gauss-seidel spectral radius is 0.9979255 estimated iterations to convergence 175 setup time was (sec) 1.110000 now iterating at: 11:04:54 rms-change max change #iterations 3.671735 146.1588 at 10iterations 1.438936 49.31437 at 20iterations 0.5664933 19.63832 at 30iterations 0.2223138 6.992294 at 40iterations 8.7523118E-02 2.827277 at 50iterations 3.4550346E-02 1.182648 at 60iterations 1.3687010E-02 0.5289936 at 70iterations 5.5508935E-03 0.1797829 at 80iterations 2.4078861E-03 9.0646744E-02 at 90iterations 1.2203148E-03 4.6658516E-02 at 100iterations 7.7347644E-04 2.8179169E-02 at 110iterations 5.6115066E-04 1.9113541E-02 at 120iterations finished qdiffx linear iterations at : 11:05:05 total time elapsed so far: 12.03000 # loops : 120 mean,max change (kT/e) : 5.6115066E-04 1.9113541E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 11:05:06 12.205u 0.513s 0:13.05 97.3% 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 11:05:06 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 = 5411 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: 2.178999 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): 43.84600 117.3660 ymin,ymax (A): -30.01600 38.72500 zmin,zma (A): -32.24100 33.62700 x,y,z range (A): 73.52000 68.74100 65.86800 scale (grids/A): 2.178999 object centre (A): 80.60600 4.354500 0.6929989 number of atom coordinates read : 5411 total number of charged atoms : 5255 net assigned charge : 10.50003 assigned positive charge : 853.6298 centred at (gu) : 88.73051 92.64382 94.59231 assigned negative charge : -843.1379 centred at (gu) : 88.52702 92.76664 94.73956 start vw surface at 0.1900000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 216406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 94049 mr = 159805 m= 20929 mr = 73787 m= 2195 mr = 14800 m= 62 mr = 1147 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 1308 time to turn everything in is 2.020000 number of dielectric boundary points 84097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 41824 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) : 1.452666 object centre at (A) : 80.60600 4.354500 0.6929989 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5019702E-02 -9.1399260E-02 midg,1,midg; midg,igrid,midg 0.3984179 -0.1071679 1,midg,midg; igrid,midg,midg -0.8470424 8.4226407E-02 gauss-seidel spectral radius is 0.9991107 estimated iterations to convergence 265 setup time was (sec) 2.400000 now iterating at: 11:05:09 rms-change max change #iterations 10.23575 287.3781 at 10iterations 5.733985 139.3331 at 20iterations 3.192478 71.01080 at 30iterations 1.770231 48.09891 at 40iterations 0.9793179 20.14564 at 50iterations 0.5378081 13.54049 at 60iterations 0.2956705 5.763165 at 70iterations 0.1622463 3.267380 at 80iterations 8.8804260E-02 1.846426 at 90iterations 4.8604365E-02 0.9947433 at 100iterations 2.6647806E-02 0.4794502 at 110iterations 1.4529500E-02 0.2896686 at 120iterations 7.9193180E-03 0.1536217 at 130iterations 4.3303198E-03 8.9136124E-02 at 140iterations 2.3698690E-03 4.6575546E-02 at 150iterations 1.2963198E-03 2.6726246E-02 at 160iterations 7.1115419E-04 1.3473511E-02 at 170iterations 3.9545316E-04 7.7972412E-03 at 180iterations finished qdiffx linear iterations at : 11:05:27 total time elapsed so far: 20.88000 # loops : 180 mean,max change (kT/e) : 3.9545316E-04 7.7972412E-03 energy calculations done at 20.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.07000 DelPhi exited at 11:05:28 21.079u 0.561s 0:21.93 98.6% 0+0k 0+0io 0pf+0w