Sun Oct 9 16:19:10 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 Sun Oct 9 2011 at 16:19:10 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 = 3104 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: 0.6286198 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): -20.42200 34.96700 ymin,ymax (A): 53.86300 106.4080 zmin,zma (A): -0.5740000 56.05800 x,y,z range (A): 55.38900 52.54501 56.63200 scale (grids/A): 0.6286198 object centre (A): 7.272500 80.13550 27.74200 number of atom coordinates read : 3104 total number of charged atoms : 2962 net assigned charge : -2.499987 assigned positive charge : 462.0429 centred at (gu) : 91.02716 90.30000 90.00112 assigned negative charge : -464.5443 centred at (gu) : 91.00813 90.20139 90.11034 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8091 nv = 96 ne = 84 npr = 63472 no. pairs analyzed = 63472 no. exposed pairs = 4019 no. arc points = 28176 no. surface atoms = 1347 nbur = 1757 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4241 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2200000 number of dielectric boundary points 4229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2778 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9929 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3273299E-09 -1.3907655E-08 midg,1,midg; midg,igrid,midg -1.1985174E-08 7.7858342E-09 1,midg,midg; igrid,midg,midg -3.6876839E-09 -8.6563579E-10 gauss-seidel spectral radius is 0.9869395 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 16:19:11 rms-change max change #iterations 0.1466531 20.42126 at 10iterations 1.4014501E-02 1.976726 at 20iterations 1.3805251E-03 0.1730347 at 30iterations 1.8609666E-04 2.0824432E-02 at 40iterations 4.0875944E-05 4.9285889E-03 at 50iterations finished qdiffx linear iterations at : 16:19:14 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.0875944E-05 4.9285889E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 16:19:14 3.424u 0.193s 0:03.88 93.0% 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 Sun Oct 9 2011 at 16:19:14 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 = 3104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.885860 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): -20.42200 34.96700 ymin,ymax (A): 53.86300 106.4080 zmin,zma (A): -0.5740000 56.05800 x,y,z range (A): 55.38900 52.54501 56.63200 scale (grids/A): 1.885860 object centre (A): 7.272500 80.13550 27.74200 number of atom coordinates read : 3104 total number of charged atoms : 2962 net assigned charge : -2.499987 assigned positive charge : 462.0429 centred at (gu) : 93.08051 90.89887 90.00262 assigned negative charge : -464.5443 centred at (gu) : 93.02409 90.60386 90.33072 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28176 grid for indexing accessible points = 1.400000 m= 30353 mr = 59809 m= 4811 mr = 21321 m= 219 mr = 2873 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 721 time to turn everything in is 0.4300000 number of dielectric boundary points 39084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 23263 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) : 0.6286198 object centre at (A) : 7.272500 80.13550 27.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9540482E-02 -1.9535899E-02 midg,1,midg; midg,igrid,midg -1.6504897E-02 -2.0773208E-02 1,midg,midg; igrid,midg,midg -9.3661156E-03 -3.0551324E-02 gauss-seidel spectral radius is 0.9986643 estimated iterations to convergence 217 setup time was (sec) 0.6500000 now iterating at: 16:19:15 rms-change max change #iterations 4.596263 193.6311 at 10iterations 2.158100 64.20424 at 20iterations 1.022411 33.23174 at 30iterations 0.4798727 15.03613 at 40iterations 0.2262185 6.299549 at 50iterations 0.1068999 3.283768 at 60iterations 5.0460927E-02 1.641079 at 70iterations 2.3811752E-02 0.6891814 at 80iterations 1.1276880E-02 0.3561821 at 90iterations 5.3219427E-03 0.1698796 at 100iterations 2.5157717E-03 7.3035836E-02 at 110iterations 1.1960985E-03 3.4806252E-02 at 120iterations finished qdiffx linear iterations at : 16:19:22 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.1960985E-03 3.4806252E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 16:19:22 8.004u 0.209s 0:08.47 96.8% 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 Sun Oct 9 2011 at 16:19:22 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 = 3104 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: 2.828789 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): -20.42200 34.96700 ymin,ymax (A): 53.86300 106.4080 zmin,zma (A): -0.5740000 56.05800 x,y,z range (A): 55.38900 52.54501 56.63200 scale (grids/A): 2.828789 object centre (A): 7.272500 80.13550 27.74200 number of atom coordinates read : 3104 total number of charged atoms : 2962 net assigned charge : -2.499987 assigned positive charge : 462.0429 centred at (gu) : 94.62072 91.34805 90.00373 assigned negative charge : -464.5443 centred at (gu) : 94.53613 90.90563 90.49603 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 203114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28176 grid for indexing accessible points = 1.400000 m= 98184 mr = 145708 m= 35480 mr = 78126 m= 8525 mr = 27633 m= 1045 mr = 6227 m= 44 mr = 654 m= 0 mr = 11 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 2053 time to turn everything in is 1.090000 number of dielectric boundary points 88033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 23696 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) : 1.885860 object centre at (A) : 7.272500 80.13550 27.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9029203 -0.2407884 midg,1,midg; midg,igrid,midg -0.2022331 -0.4144812 1,midg,midg; igrid,midg,midg -0.1029733 -0.4964138 gauss-seidel spectral radius is 0.9992861 estimated iterations to convergence 295 setup time was (sec) 1.340000 now iterating at: 16:19:24 rms-change max change #iterations 10.92350 344.7383 at 10iterations 6.535895 140.9772 at 20iterations 3.872066 85.13251 at 30iterations 2.288574 46.50807 at 40iterations 1.344283 28.15774 at 50iterations 0.7905434 15.58665 at 60iterations 0.4626656 8.528801 at 70iterations 0.2711330 4.863682 at 80iterations 0.1581844 2.914765 at 90iterations 9.2345946E-02 1.816244 at 100iterations 5.3854086E-02 0.9532852 at 110iterations 3.1425342E-02 0.5654831 at 120iterations 1.8272098E-02 0.3122902 at 130iterations 1.0635633E-02 0.2018356 at 140iterations 6.1939871E-03 0.1012611 at 150iterations 3.6101723E-03 6.9122314E-02 at 160iterations 2.0951342E-03 3.5720825E-02 at 170iterations 1.2200343E-03 2.0401001E-02 at 180iterations finished qdiffx linear iterations at : 16:19:35 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 1.2200343E-03 2.0401001E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 16:19:36 12.922u 0.209s 0:13.39 97.9% 0+0k 0+0io 0pf+0w