Sun Oct 9 01:10:55 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 01:10:55 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 = 2262 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: 0.6461214 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): -26.76200 26.64700 ymin,ymax (A): 7.932000 51.75500 zmin,zma (A): -13.82400 41.27400 x,y,z range (A): 53.40900 43.82300 55.09800 scale (grids/A): 0.6461214 object centre (A): -5.7498932E-02 29.84350 13.72500 number of atom coordinates read : 2262 total number of charged atoms : 2127 net assigned charge : 10.50003 assigned positive charge : 328.0597 centred at (gu) : 90.54615 90.27843 91.58800 assigned negative charge : -317.5602 centred at (gu) : 90.50473 90.21548 91.63422 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6437 nv = 96 ne = 84 npr = 45174 no. pairs analyzed = 45174 no. exposed pairs = 3056 no. arc points = 22298 no. surface atoms = 1004 nbur = 1258 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3297 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.3500000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2127 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7591 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6855839E-08 1.7871919E-08 midg,1,midg; midg,igrid,midg 1.0482792E-08 2.6714408E-08 1,midg,midg; igrid,midg,midg 1.2119772E-08 2.5559791E-08 gauss-seidel spectral radius is 0.9875686 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 01:10:56 rms-change max change #iterations 0.1366072 19.37358 at 10iterations 1.3535156E-02 2.190783 at 20iterations 1.3380756E-03 0.1925621 at 30iterations 1.3967972E-04 2.1814346E-02 at 40iterations 1.4954065E-05 2.2048950E-03 at 50iterations finished qdiffx linear iterations at : 01:11:00 total time elapsed so far: 4.630000 # loops : 50 mean,max change (kT/e) : 1.4954065E-05 2.2048950E-03 energy calculations done at 4.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.850000 DelPhi exited at 01:11:01 4.855u 0.473s 0:05.65 94.1% 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 01:11:01 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 = 2262 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: 1.938364 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): -26.76200 26.64700 ymin,ymax (A): 7.932000 51.75500 zmin,zma (A): -13.82400 41.27400 x,y,z range (A): 53.40900 43.82300 55.09800 scale (grids/A): 1.938364 object centre (A): -5.7498932E-02 29.84350 13.72500 number of atom coordinates read : 2262 total number of charged atoms : 2127 net assigned charge : 10.50003 assigned positive charge : 328.0597 centred at (gu) : 91.63805 90.83513 94.76371 assigned negative charge : -317.5602 centred at (gu) : 91.51441 90.64649 94.90277 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 68842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22298 grid for indexing accessible points = 1.400000 m= 24285 mr = 45114 m= 4266 mr = 17321 m= 342 mr = 2654 m= 3 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2680 time to turn everything in is 0.7200000 number of dielectric boundary points 32503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 16737 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) : 0.6461214 object centre at (A) : -5.7498932E-02 29.84350 13.72500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5150172E-02 2.6224466E-02 midg,1,midg; midg,igrid,midg -1.9118295E-03 2.1572812E-02 1,midg,midg; igrid,midg,midg 4.7991022E-02 6.1245020E-02 gauss-seidel spectral radius is 0.9986599 estimated iterations to convergence 216 setup time was (sec) 1.080000 now iterating at: 01:11:02 rms-change max change #iterations 3.918511 180.6849 at 10iterations 1.836818 63.81944 at 20iterations 0.8672356 31.57516 at 30iterations 0.4062452 13.53603 at 40iterations 0.1909404 6.362295 at 50iterations 8.9820102E-02 3.091900 at 60iterations 4.2354532E-02 1.345501 at 70iterations 1.9876871E-02 0.6739979 at 80iterations 9.3388706E-03 0.3192616 at 90iterations 4.4033481E-03 0.1364079 at 100iterations 2.0690651E-03 8.1177711E-02 at 110iterations 9.7945472E-04 3.3062935E-02 at 120iterations finished qdiffx linear iterations at : 01:11:12 total time elapsed so far: 11.26000 # loops : 120 mean,max change (kT/e) : 9.7945472E-04 3.3062935E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 01:11:13 11.491u 0.488s 0:12.29 97.3% 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 01:11:13 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 = 2262 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: 2.907547 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): -26.76200 26.64700 ymin,ymax (A): 7.932000 51.75500 zmin,zma (A): -13.82400 41.27400 x,y,z range (A): 53.40900 43.82300 55.09800 scale (grids/A): 2.907547 object centre (A): -5.7498932E-02 29.84350 13.72500 number of atom coordinates read : 2262 total number of charged atoms : 2127 net assigned charge : 10.50003 assigned positive charge : 328.0597 centred at (gu) : 92.45694 91.25275 97.14549 assigned negative charge : -317.5602 centred at (gu) : 92.27174 90.96985 97.35426 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 158810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22298 grid for indexing accessible points = 1.400000 m= 77818 mr = 109930 m= 29028 mr = 62031 m= 7776 mr = 22965 m= 1402 mr = 5736 m= 103 mr = 944 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 9050 time to turn everything in is 1.880000 number of dielectric boundary points 73280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 17016 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) : 1.938364 object centre at (A) : -5.7498932E-02 29.84350 13.72500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6464015 0.3116686 midg,1,midg; midg,igrid,midg -2.0284394E-02 0.2062151 1,midg,midg; igrid,midg,midg 0.5458976 0.5919220 gauss-seidel spectral radius is 0.9992720 estimated iterations to convergence 292 setup time was (sec) 2.250000 now iterating at: 01:11:16 rms-change max change #iterations 9.355176 436.0688 at 10iterations 5.525280 137.1211 at 20iterations 3.233053 72.49662 at 30iterations 1.886904 40.12486 at 40iterations 1.098767 20.61326 at 50iterations 0.6387870 12.18592 at 60iterations 0.3704845 7.379969 at 70iterations 0.2153014 4.449685 at 80iterations 0.1244627 2.251123 at 90iterations 7.2209708E-02 1.348308 at 100iterations 4.1761361E-02 0.8650837 at 110iterations 2.4143245E-02 0.5198355 at 120iterations 1.3959645E-02 0.2859150 at 130iterations 8.0427863E-03 0.1546955 at 140iterations 4.6474854E-03 8.5348129E-02 at 150iterations 2.6867273E-03 5.2845001E-02 at 160iterations 1.5521835E-03 2.8831482E-02 at 170iterations 8.9360983E-04 1.6760826E-02 at 180iterations finished qdiffx linear iterations at : 01:11:33 total time elapsed so far: 19.17000 # loops : 180 mean,max change (kT/e) : 8.9360983E-04 1.6760826E-02 energy calculations done at 19.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.37000 DelPhi exited at 01:11:33 19.376u 0.562s 0:20.20 98.6% 0+0k 0+0io 0pf+0w