Tue Oct 11 03:17:18 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 03:17:18 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 0.6723450 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): -7.181000 44.09600 ymin,ymax (A): 0.1969999 53.14600 zmin,zma (A): 13.33100 65.86800 x,y,z range (A): 51.27700 52.94900 52.53699 scale (grids/A): 0.6723450 object centre (A): 18.45750 26.67150 39.59950 number of atom coordinates read : 2366 total number of charged atoms : 2271 net assigned charge : 1.000011 assigned positive charge : 355.3250 centred at (gu) : 87.49487 89.98470 89.30654 assigned negative charge : -354.3255 centred at (gu) : 87.50766 90.20922 89.24101 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7500 nv = 96 ne = 84 npr = 46314 no. pairs analyzed = 46314 no. exposed pairs = 3240 no. arc points = 23695 no. surface atoms = 1087 nbur = 1279 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 3867 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2119 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8567 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4531850E-08 1.6928260E-08 midg,1,midg; midg,igrid,midg 5.7440168E-08 -5.2454766E-08 1,midg,midg; igrid,midg,midg 1.1271369E-08 3.4416747E-10 gauss-seidel spectral radius is 0.9885258 estimated iterations to convergence 76 setup time was (sec) 0.5700000 now iterating at: 03:17:19 rms-change max change #iterations 0.1765262 27.78963 at 10iterations 1.9436579E-02 2.698639 at 20iterations 2.1991669E-03 0.2912369 at 30iterations 2.7606299E-04 4.4713497E-02 at 40iterations 5.0102310E-05 9.7713470E-03 at 50iterations finished qdiffx linear iterations at : 03:17:22 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 5.0102310E-05 9.7713470E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 03:17:22 3.581u 0.174s 0:04.14 90.5% 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 03:17:22 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 2.017035 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): -7.181000 44.09600 ymin,ymax (A): 0.1969999 53.14600 zmin,zma (A): 13.33100 65.86800 x,y,z range (A): 51.27700 52.94900 52.53699 scale (grids/A): 2.017035 object centre (A): 18.45750 26.67150 39.59950 number of atom coordinates read : 2366 total number of charged atoms : 2271 net assigned charge : 1.000011 assigned positive charge : 355.3250 centred at (gu) : 82.48418 89.95364 87.91936 assigned negative charge : -354.3255 centred at (gu) : 82.52275 90.62755 87.72270 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23695 grid for indexing accessible points = 1.400000 m= 29677 mr = 52982 m= 5525 mr = 21487 m= 401 mr = 3400 m= 6 mr = 142 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 37157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17994 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) : 0.6723450 object centre at (A) : 18.45750 26.67150 39.59950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4598581E-02 1.9282794E-02 midg,1,midg; midg,igrid,midg 2.8862085E-02 -8.5941717E-02 1,midg,midg; igrid,midg,midg -7.2389534E-03 4.8500514E-03 gauss-seidel spectral radius is 0.9987689 estimated iterations to convergence 226 setup time was (sec) 0.9200000 now iterating at: 03:17:24 rms-change max change #iterations 4.510841 203.3632 at 10iterations 2.189137 81.82599 at 20iterations 1.064677 30.84929 at 30iterations 0.5198702 16.02069 at 40iterations 0.2532504 7.690514 at 50iterations 0.1228749 3.510039 at 60iterations 5.9811067E-02 2.174043 at 70iterations 2.8994413E-02 0.8830776 at 80iterations 1.4152633E-02 0.4443035 at 90iterations 6.9041038E-03 0.2294693 at 100iterations 3.3752308E-03 9.7696304E-02 at 110iterations 1.6462321E-03 4.9006462E-02 at 120iterations finished qdiffx linear iterations at : 03:17:31 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 1.6462321E-03 4.9006462E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 03:17:31 8.296u 0.265s 0:08.98 95.2% 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 Tue Oct 11 2011 at 03:17:31 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 3.025553 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): -7.181000 44.09600 ymin,ymax (A): 0.1969999 53.14600 zmin,zma (A): 13.33100 65.86800 x,y,z range (A): 51.27700 52.94900 52.53699 scale (grids/A): 3.025553 object centre (A): 18.45750 26.67150 39.59950 number of atom coordinates read : 2366 total number of charged atoms : 2271 net assigned charge : 1.000011 assigned positive charge : 355.3250 centred at (gu) : 78.72598 89.93024 86.87888 assigned negative charge : -354.3255 centred at (gu) : 78.78416 90.94138 86.58403 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 183605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23695 grid for indexing accessible points = 1.400000 m= 92741 mr = 128736 m= 37198 mr = 74632 m= 10147 mr = 29782 m= 1656 mr = 7432 m= 152 mr = 1083 m= 6 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 83776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 18168 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) : 2.017035 object centre at (A) : 18.45750 26.67150 39.59950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2647291 0.1522369 midg,1,midg; midg,igrid,midg 0.1977197 -0.9924406 1,midg,midg; igrid,midg,midg 7.1125567E-02 2.8185746E-02 gauss-seidel spectral radius is 0.9993089 estimated iterations to convergence 300 setup time was (sec) 1.950000 now iterating at: 03:17:34 rms-change max change #iterations 10.48401 352.8663 at 10iterations 6.286226 138.1753 at 20iterations 3.763226 72.43585 at 30iterations 2.232247 48.66047 at 40iterations 1.324794 24.41890 at 50iterations 0.7796214 13.85971 at 60iterations 0.4599271 7.761297 at 70iterations 0.2705298 5.377531 at 80iterations 0.1593903 2.597026 at 90iterations 9.3321361E-02 1.619537 at 100iterations 5.4755040E-02 0.9493275 at 110iterations 3.2114286E-02 0.5550117 at 120iterations 1.8829856E-02 0.3209820 at 130iterations 1.1041463E-02 0.1955948 at 140iterations 6.4722234E-03 0.1157856 at 150iterations 3.7949451E-03 6.8708181E-02 at 160iterations 2.2289215E-03 4.0592194E-02 at 170iterations 1.3053092E-03 2.3172379E-02 at 180iterations finished qdiffx linear iterations at : 03:17:45 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 1.3053092E-03 2.3172379E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 03:17:46 13.529u 0.263s 0:14.25 96.7% 0+0k 0+0io 0pf+0w