Sun Oct 9 16:20:32 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 16:20:32 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 = 3038 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: 0.6235004 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): -21.21000 35.09000 ymin,ymax (A): 54.47900 106.5420 zmin,zma (A): -1.523000 55.57400 x,y,z range (A): 56.30000 52.06300 57.09700 scale (grids/A): 0.6235004 object centre (A): 6.940001 80.51050 27.02550 number of atom coordinates read : 3038 total number of charged atoms : 2896 net assigned charge : -2.499989 assigned positive charge : 452.8990 centred at (gu) : 91.04457 90.26616 90.08048 assigned negative charge : -455.4002 centred at (gu) : 91.07752 90.15292 90.21687 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7778 nv = 96 ne = 84 npr = 61511 no. pairs analyzed = 61511 no. exposed pairs = 3981 no. arc points = 27816 no. surface atoms = 1336 nbur = 1702 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 4068 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2300000 number of dielectric boundary points 4122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2658 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2069623E-09 -1.4403942E-08 midg,1,midg; midg,igrid,midg -1.1404897E-08 7.8979863E-09 1,midg,midg; igrid,midg,midg 4.7274173E-10 -6.3641257E-09 gauss-seidel spectral radius is 0.9867193 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 16:20:33 rms-change max change #iterations 0.1360093 18.65130 at 10iterations 1.2771646E-02 2.135027 at 20iterations 1.2662358E-03 0.1664047 at 30iterations 1.9296297E-04 2.1568298E-02 at 40iterations 5.1928262E-05 5.4416656E-03 at 50iterations finished qdiffx linear iterations at : 16:20:36 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.1928262E-05 5.4416656E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 16:20:36 3.364u 0.169s 0:03.79 92.8% 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 16:20:36 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 = 3038 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: 1.870501 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): -21.21000 35.09000 ymin,ymax (A): 54.47900 106.5420 zmin,zma (A): -1.523000 55.57400 x,y,z range (A): 56.30000 52.06300 57.09700 scale (grids/A): 1.870501 object centre (A): 6.940001 80.51050 27.02550 number of atom coordinates read : 3038 total number of charged atoms : 2896 net assigned charge : -2.499989 assigned positive charge : 452.8990 centred at (gu) : 93.13296 90.79741 90.24104 assigned negative charge : -455.4002 centred at (gu) : 93.23253 90.45878 90.65009 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27816 grid for indexing accessible points = 1.400000 m= 29177 mr = 57179 m= 4744 mr = 20352 m= 256 mr = 2889 m= 0 mr = 99 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1486 time to turn everything in is 0.4100000 number of dielectric boundary points 37952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22726 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) : 0.6235004 object centre at (A) : 6.940001 80.51050 27.02550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7099967E-02 -2.0952454E-02 midg,1,midg; midg,igrid,midg -1.9332858E-02 -1.0004811E-02 1,midg,midg; igrid,midg,midg -8.8517135E-03 -4.3815840E-02 gauss-seidel spectral radius is 0.9986368 estimated iterations to convergence 215 setup time was (sec) 0.6200000 now iterating at: 16:20:37 rms-change max change #iterations 4.461042 172.4418 at 10iterations 2.074945 65.09549 at 20iterations 0.9714556 28.21244 at 30iterations 0.4561841 13.69188 at 40iterations 0.2123775 7.194718 at 50iterations 0.1000226 3.086838 at 60iterations 4.6672355E-02 1.372822 at 70iterations 2.1878056E-02 0.6481943 at 80iterations 1.0239975E-02 0.3177986 at 90iterations 4.8094606E-03 0.1439648 at 100iterations 2.2686319E-03 6.8355560E-02 at 110iterations 1.0696724E-03 3.1048775E-02 at 120iterations finished qdiffx linear iterations at : 16:20:44 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.0696724E-03 3.1048775E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 16:20:44 7.767u 0.187s 0:08.23 96.4% 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 16:20:44 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 = 3038 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: 2.805752 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): -21.21000 35.09000 ymin,ymax (A): 54.47900 106.5420 zmin,zma (A): -1.523000 55.57400 x,y,z range (A): 56.30000 52.06300 57.09700 scale (grids/A): 2.805752 object centre (A): 6.940001 80.51050 27.02550 number of atom coordinates read : 3038 total number of charged atoms : 2896 net assigned charge : -2.499989 assigned positive charge : 452.8990 centred at (gu) : 94.69942 91.19586 90.36147 assigned negative charge : -455.4002 centred at (gu) : 94.84878 90.68814 90.97522 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 195286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27816 grid for indexing accessible points = 1.400000 m= 94014 mr = 139173 m= 33857 mr = 74405 m= 8518 mr = 26505 m= 1215 mr = 6354 m= 64 mr = 816 m= 0 mr = 22 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 5033 time to turn everything in is 1.050000 number of dielectric boundary points 85679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 23166 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) : 1.870501 object centre at (A) : 6.940001 80.51050 27.02550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8872516 -0.2907206 midg,1,midg; midg,igrid,midg -0.2044843 -0.2856927 1,midg,midg; igrid,midg,midg -0.1189018 -0.5997180 gauss-seidel spectral radius is 0.9992773 estimated iterations to convergence 294 setup time was (sec) 1.300000 now iterating at: 16:20:46 rms-change max change #iterations 10.73081 317.4265 at 10iterations 6.423583 148.8735 at 20iterations 3.815839 87.39586 at 30iterations 2.251213 50.32909 at 40iterations 1.323440 29.51924 at 50iterations 0.7757356 15.90241 at 60iterations 0.4538645 10.33123 at 70iterations 0.2645539 4.896564 at 80iterations 0.1545771 2.761750 at 90iterations 9.0054497E-02 1.887727 at 100iterations 5.2456230E-02 1.053162 at 110iterations 3.0450156E-02 0.6502337 at 120iterations 1.7680682E-02 0.3508301 at 130iterations 1.0278426E-02 0.1742134 at 140iterations 5.9568333E-03 0.1179733 at 150iterations 3.4626736E-03 6.9180489E-02 at 160iterations 2.0056651E-03 3.6584854E-02 at 170iterations 1.1630043E-03 2.0576477E-02 at 180iterations finished qdiffx linear iterations at : 16:20:57 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.1630043E-03 2.0576477E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 16:20:58 12.872u 0.199s 0:13.39 97.5% 0+0k 0+0io 0pf+0w