Sat Oct 15 11:18:30 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 Sat Oct 15 2011 at 11:18:30 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 = 3585 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: 0.5685993 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): 12.02000 74.63000 ymin,ymax (A): -1.283000 50.94100 zmin,zma (A): 22.51600 77.60700 x,y,z range (A): 62.61000 52.22400 55.09100 scale (grids/A): 0.5685993 object centre (A): 43.32500 24.82900 50.06150 number of atom coordinates read : 3585 total number of charged atoms : 3465 net assigned charge : -3.499971 assigned positive charge : 550.3247 centred at (gu) : 88.40102 91.22108 89.52863 assigned negative charge : -553.8262 centred at (gu) : 88.49393 91.07951 89.51691 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7462 nv = 96 ne = 84 npr = 73256 no. pairs analyzed = 73256 no. exposed pairs = 4107 no. arc points = 28583 no. surface atoms = 1390 nbur = 2195 mkacc time = 0.2400000 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 = 1.512000 m= 271 mr = 4237 m= 0 mr = 15 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.5000000 number of dielectric boundary points 3481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2841 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 9660 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8195301E-10 -3.1806049E-10 midg,1,midg; midg,igrid,midg -2.4246400E-09 2.7250555E-09 1,midg,midg; igrid,midg,midg 1.6946567E-09 -1.5837044E-09 gauss-seidel spectral radius is 0.9840798 estimated iterations to convergence 65 setup time was (sec) 0.8100000 now iterating at: 11:18:31 rms-change max change #iterations 0.1032250 16.00023 at 10iterations 7.7832136E-03 1.081276 at 20iterations 5.9883203E-04 8.1429482E-02 at 30iterations 5.2221480E-05 7.8916550E-03 at 40iterations 7.4894638E-06 1.3937950E-03 at 50iterations finished qdiffx linear iterations at : 11:18:35 total time elapsed so far: 4.830000 # loops : 50 mean,max change (kT/e) : 7.4894638E-06 1.3937950E-03 energy calculations done at 4.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.050000 DelPhi exited at 11:18:36 5.057u 0.440s 0:06.04 90.8% 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 Sat Oct 15 2011 at 11:18:36 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 = 3585 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: 1.705798 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): 12.02000 74.63000 ymin,ymax (A): -1.283000 50.94100 zmin,zma (A): 22.51600 77.60700 x,y,z range (A): 62.61000 52.22400 55.09100 scale (grids/A): 1.705798 object centre (A): 43.32500 24.82900 50.06150 number of atom coordinates read : 3585 total number of charged atoms : 3465 net assigned charge : -3.499971 assigned positive charge : 550.3247 centred at (gu) : 85.20222 93.66209 88.58501 assigned negative charge : -553.8262 centred at (gu) : 85.48144 93.23798 88.55025 start vw surface at 0.1900000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 82947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28583 grid for indexing accessible points = 1.400000 m= 27500 mr = 59187 m= 3019 mr = 20424 m= 98 mr = 1699 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2278 time to turn everything in is 0.8300000 number of dielectric boundary points 32228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 26818 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) : 0.5685993 object centre at (A) : 43.32500 24.82900 50.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1305023E-02 -7.1478458E-03 midg,1,midg; midg,igrid,midg -1.6180217E-02 1.5096566E-02 1,midg,midg; igrid,midg,midg 6.9701835E-03 -8.2516810E-03 gauss-seidel spectral radius is 0.9983913 estimated iterations to convergence 198 setup time was (sec) 1.200000 now iterating at: 11:18:37 rms-change max change #iterations 4.138697 158.0371 at 10iterations 1.820132 53.09900 at 20iterations 0.7993615 26.24868 at 30iterations 0.3517216 12.72153 at 40iterations 0.1547400 5.019132 at 50iterations 6.8077765E-02 2.081484 at 60iterations 2.9980371E-02 0.9100752 at 70iterations 1.3156310E-02 0.4004021 at 80iterations 5.8077355E-03 0.1996615 at 90iterations 2.5514560E-03 8.7507486E-02 at 100iterations 1.1239687E-03 3.6340952E-02 at 110iterations 4.9542758E-04 1.6128540E-02 at 120iterations finished qdiffx linear iterations at : 11:18:48 total time elapsed so far: 12.14000 # loops : 120 mean,max change (kT/e) : 4.9542758E-04 1.6128540E-02 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 11:18:49 12.368u 0.496s 0:13.40 95.8% 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 Sat Oct 15 2011 at 11:18:49 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 = 3585 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: 2.558697 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): 12.02000 74.63000 ymin,ymax (A): -1.283000 50.94100 zmin,zma (A): 22.51600 77.60700 x,y,z range (A): 62.61000 52.22400 55.09100 scale (grids/A): 2.558697 object centre (A): 43.32500 24.82900 50.06150 number of atom coordinates read : 3585 total number of charged atoms : 3465 net assigned charge : -3.499971 assigned positive charge : 550.3247 centred at (gu) : 82.80293 95.49306 87.87701 assigned negative charge : -553.8262 centred at (gu) : 83.22203 94.85697 87.82516 start vw surface at 0.1900000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 192882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28583 grid for indexing accessible points = 1.400000 m= 93411 mr = 143872 m= 28775 mr = 77081 m= 5054 mr = 23134 m= 412 mr = 3614 m= 14 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 7378 time to turn everything in is 2.100000 number of dielectric boundary points 72603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 27700 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) : 1.705798 object centre at (A) : 43.32500 24.82900 50.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1935922 -0.1146464 midg,1,midg; midg,igrid,midg -0.1809148 0.1441109 1,midg,midg; igrid,midg,midg 5.6483403E-02 -4.7361296E-02 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 2.490000 now iterating at: 11:18:52 rms-change max change #iterations 10.16752 277.3754 at 10iterations 5.782478 124.1172 at 20iterations 3.273046 72.21702 at 30iterations 1.854525 37.98626 at 40iterations 1.043923 20.95555 at 50iterations 0.5888463 11.33848 at 60iterations 0.3311311 6.150456 at 70iterations 0.1861654 3.301389 at 80iterations 0.1048592 1.889640 at 90iterations 5.8885887E-02 1.181063 at 100iterations 3.3108264E-02 0.6186638 at 110iterations 1.8629912E-02 0.3719025 at 120iterations 1.0495177E-02 0.1908302 at 130iterations 5.8992445E-03 0.1069946 at 140iterations 3.3111011E-03 5.6446075E-02 at 150iterations 1.8606110E-03 3.4690857E-02 at 160iterations 1.0464713E-03 1.9609213E-02 at 170iterations 5.8795139E-04 1.1211395E-02 at 180iterations finished qdiffx linear iterations at : 11:19:10 total time elapsed so far: 20.24000 # loops : 180 mean,max change (kT/e) : 5.8795139E-04 1.1211395E-02 energy calculations done at 20.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.45000 DelPhi exited at 11:19:11 20.457u 0.523s 0:21.45 97.7% 0+0k 0+0io 0pf+0w