Sun Oct 9 09:35:15 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 09:35:15 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 = 2815 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: 0.5511860 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): -79.62100 -30.89300 ymin,ymax (A): -36.80700 27.78100 zmin,zma (A): -51.50300 1.918000 x,y,z range (A): 48.72800 64.58800 53.42100 scale (grids/A): 0.5511860 object centre (A): -55.25700 -4.513000 -24.79250 number of atom coordinates read : 2815 total number of charged atoms : 2668 net assigned charge : 2.0243227E-05 assigned positive charge : 414.8905 centred at (gu) : 89.34464 88.97707 89.42264 assigned negative charge : -414.8914 centred at (gu) : 89.34956 89.18204 89.52704 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5760 nv = 96 ne = 84 npr = 55105 no. pairs analyzed = 55105 no. exposed pairs = 3901 no. arc points = 27931 no. surface atoms = 1291 nbur = 1524 mkacc time = 9.0000004E-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 = 1.568000 m= 274 mr = 2814 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2746 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7355 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7082069E-10 -7.0659290E-10 midg,1,midg; midg,igrid,midg 1.9141986E-09 -1.2419852E-09 1,midg,midg; igrid,midg,midg 1.8949868E-11 -4.9185496E-11 gauss-seidel spectral radius is 0.9830242 estimated iterations to convergence 63 setup time was (sec) 0.3800000 now iterating at: 09:35:16 rms-change max change #iterations 7.1529165E-02 12.09853 at 10iterations 4.9575986E-03 0.8007317 at 20iterations 3.5023919E-04 7.3044777E-02 at 30iterations 3.8204133E-05 8.0709457E-03 at 40iterations 9.0414251E-06 2.3059845E-03 at 50iterations finished qdiffx linear iterations at : 09:35:19 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 9.0414251E-06 2.3059845E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 09:35:19 3.348u 0.188s 0:03.82 92.1% 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 09:35:19 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 = 2815 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: 1.653558 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): -79.62100 -30.89300 ymin,ymax (A): -36.80700 27.78100 zmin,zma (A): -51.50300 1.918000 x,y,z range (A): 48.72800 64.58800 53.42100 scale (grids/A): 1.653558 object centre (A): -55.25700 -4.513000 -24.79250 number of atom coordinates read : 2815 total number of charged atoms : 2668 net assigned charge : 2.0243227E-05 assigned positive charge : 414.8905 centred at (gu) : 88.03320 86.93052 88.26762 assigned negative charge : -414.8914 centred at (gu) : 88.04818 87.54592 88.58083 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27931 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20010 mr = 41049 m= 2196 mr = 13524 m= 70 mr = 1035 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3100000 number of dielectric boundary points 29587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20501 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) : 0.5511860 object centre at (A) : -55.25700 -4.513000 -24.79250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5510988E-03 -9.7847888E-03 midg,1,midg; midg,igrid,midg -4.9035070E-03 -1.0087635E-02 1,midg,midg; igrid,midg,midg 6.6938298E-03 6.0511874E-03 gauss-seidel spectral radius is 0.9982305 estimated iterations to convergence 189 setup time was (sec) 0.5300000 now iterating at: 09:35:20 rms-change max change #iterations 3.266982 154.8641 at 10iterations 1.367436 54.61546 at 20iterations 0.5744889 21.23403 at 30iterations 0.2419832 8.517200 at 40iterations 0.1011416 3.445989 at 50iterations 4.2660184E-02 1.602894 at 60iterations 1.7988633E-02 0.6360359 at 70iterations 7.5735198E-03 0.2801890 at 80iterations 3.2185088E-03 0.1218452 at 90iterations 1.3629966E-03 5.5995703E-02 at 100iterations 5.8557600E-04 2.2148132E-02 at 110iterations 2.5927386E-04 1.0706425E-02 at 120iterations finished qdiffx linear iterations at : 09:35:27 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.5927386E-04 1.0706425E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 09:35:27 7.617u 0.208s 0:08.19 95.3% 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 Sun Oct 9 2011 at 09:35:27 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 = 2815 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: 2.480337 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): -79.62100 -30.89300 ymin,ymax (A): -36.80700 27.78100 zmin,zma (A): -51.50300 1.918000 x,y,z range (A): 48.72800 64.58800 53.42100 scale (grids/A): 2.480337 object centre (A): -55.25700 -4.513000 -24.79250 number of atom coordinates read : 2815 total number of charged atoms : 2668 net assigned charge : 2.0243227E-05 assigned positive charge : 414.8905 centred at (gu) : 87.04981 85.39557 87.40115 assigned negative charge : -414.8914 centred at (gu) : 87.07230 86.31890 87.87123 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 145988 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27931 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67817 mr = 100955 m= 20584 mr = 52865 m= 3468 mr = 15193 m= 239 mr = 2183 m= 5 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 0.7700000 number of dielectric boundary points 66801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21330 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) : 1.653558 object centre at (A) : -55.25700 -4.513000 -24.79250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4041456E-02 -0.1371892 midg,1,midg; midg,igrid,midg -0.2250075 -8.1637144E-02 1,midg,midg; igrid,midg,midg 0.1063394 9.9381849E-02 gauss-seidel spectral radius is 0.9991558 estimated iterations to convergence 272 setup time was (sec) 1.010000 now iterating at: 09:35:29 rms-change max change #iterations 8.599102 286.9080 at 10iterations 4.894269 160.1704 at 20iterations 2.774563 70.22462 at 30iterations 1.555953 37.21472 at 40iterations 0.8718099 20.91941 at 50iterations 0.4867750 11.85295 at 60iterations 0.2718205 6.955811 at 70iterations 0.1506812 3.561933 at 80iterations 8.3905451E-02 2.313637 at 90iterations 4.6501372E-02 0.9890184 at 100iterations 2.5813797E-02 0.5952111 at 110iterations 1.4273356E-02 0.3030357 at 120iterations 7.9075620E-03 0.1782570 at 130iterations 4.3785167E-03 0.1028913 at 140iterations 2.4146647E-03 5.5492401E-02 at 150iterations 1.3378594E-03 2.9947758E-02 at 160iterations 7.4122270E-04 1.5899658E-02 at 170iterations 4.1003272E-04 8.2054138E-03 at 180iterations finished qdiffx linear iterations at : 09:35:40 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 4.1003272E-04 8.2054138E-03 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 09:35:40 12.208u 0.202s 0:12.68 97.7% 0+0k 0+0io 0pf+0w