Sat Oct 15 12:12:27 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 12:12:27 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 = 2283 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: 0.6543757 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): -27.34200 27.06100 ymin,ymax (A): 8.113999 52.10300 zmin,zma (A): -12.60500 41.37900 x,y,z range (A): 54.40300 43.98900 53.98400 scale (grids/A): 0.6543757 object centre (A): -0.1405010 30.10850 14.38700 number of atom coordinates read : 2283 total number of charged atoms : 2149 net assigned charge : 10.50002 assigned positive charge : 330.2657 centred at (gu) : 90.54450 90.53989 91.37342 assigned negative charge : -319.7662 centred at (gu) : 90.53883 90.49175 91.36063 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6762 nv = 96 ne = 84 npr = 45564 no. pairs analyzed = 45564 no. exposed pairs = 3095 no. arc points = 22410 no. surface atoms = 1039 nbur = 1244 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 3459 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.1800000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2153 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5943023E-08 3.2542143E-08 midg,1,midg; midg,igrid,midg 1.4358163E-08 3.2968792E-08 1,midg,midg; igrid,midg,midg 1.9692882E-08 2.6325804E-08 gauss-seidel spectral radius is 0.9878796 estimated iterations to convergence 74 setup time was (sec) 0.4200000 now iterating at: 12:12:27 rms-change max change #iterations 0.1415653 21.24919 at 10iterations 1.4302782E-02 2.028284 at 20iterations 1.5240579E-03 0.2896858 at 30iterations 1.5820231E-04 2.1850586E-02 at 40iterations 1.6948758E-05 2.6426315E-03 at 50iterations finished qdiffx linear iterations at : 12:12:31 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 1.6948758E-05 2.6426315E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 12:12:31 3.985u 0.249s 0:04.56 92.5% 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 Sat Oct 15 2011 at 12:12:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 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: 1.963127 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): -27.34200 27.06100 ymin,ymax (A): 8.113999 52.10300 zmin,zma (A): -12.60500 41.37900 x,y,z range (A): 54.40300 43.98900 53.98400 scale (grids/A): 1.963127 object centre (A): -0.1405010 30.10850 14.38700 number of atom coordinates read : 2283 total number of charged atoms : 2149 net assigned charge : 10.50002 assigned positive charge : 330.2657 centred at (gu) : 91.63331 91.61964 94.12015 assigned negative charge : -319.7662 centred at (gu) : 91.61669 91.47538 94.08231 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 72221 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22410 grid for indexing accessible points = 1.400000 m= 25620 mr = 47703 m= 4174 mr = 18226 m= 263 mr = 2395 m= 6 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 348 time to turn everything in is 0.3600000 number of dielectric boundary points 33869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 16953 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) : 0.6543757 object centre at (A) : -0.1405010 30.10850 14.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9846361E-02 3.3671983E-02 midg,1,midg; midg,igrid,midg 5.4980902E-04 2.1775652E-02 1,midg,midg; igrid,midg,midg 5.1147085E-02 6.1910316E-02 gauss-seidel spectral radius is 0.9986929 estimated iterations to convergence 219 setup time was (sec) 0.6400000 now iterating at: 12:12:32 rms-change max change #iterations 4.040252 193.5743 at 10iterations 1.915143 69.92319 at 20iterations 0.9073061 28.51545 at 30iterations 0.4322487 13.87399 at 40iterations 0.2050545 6.346088 at 50iterations 9.7474009E-02 3.401701 at 60iterations 4.6212722E-02 1.492653 at 70iterations 2.2095786E-02 0.6517906 at 80iterations 1.0461627E-02 0.3287716 at 90iterations 4.9856785E-03 0.1527643 at 100iterations 2.3591889E-03 7.3097229E-02 at 110iterations 1.1255227E-03 3.6808014E-02 at 120iterations finished qdiffx linear iterations at : 12:12:40 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 1.1255227E-03 3.6808014E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 12:12:41 9.043u 0.316s 0:09.74 95.9% 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 12:12:41 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 = 2283 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: 2.944690 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): -27.34200 27.06100 ymin,ymax (A): 8.113999 52.10300 zmin,zma (A): -12.60500 41.37900 x,y,z range (A): 54.40300 43.98900 53.98400 scale (grids/A): 2.944690 object centre (A): -0.1405010 30.10850 14.38700 number of atom coordinates read : 2283 total number of charged atoms : 2149 net assigned charge : 10.50002 assigned positive charge : 330.2657 centred at (gu) : 92.44982 92.42938 96.18015 assigned negative charge : -319.7662 centred at (gu) : 92.42511 92.21307 96.12352 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 166409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22410 grid for indexing accessible points = 1.400000 m= 82401 mr = 116022 m= 29909 mr = 65697 m= 7318 mr = 23247 m= 1191 mr = 5241 m= 62 mr = 749 m= 0 mr = 13 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1103 time to turn everything in is 1.000000 number of dielectric boundary points 76321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17189 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) : 1.963127 object centre at (A) : -0.1405010 30.10850 14.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6285186 0.3614308 midg,1,midg; midg,igrid,midg 1.1905646E-02 0.2031987 1,midg,midg; igrid,midg,midg 0.5473981 0.6063181 gauss-seidel spectral radius is 0.9992833 estimated iterations to convergence 295 setup time was (sec) 1.300000 now iterating at: 12:12:43 rms-change max change #iterations 9.580639 422.2543 at 10iterations 5.676586 149.1362 at 20iterations 3.351730 78.31935 at 30iterations 1.968601 45.69131 at 40iterations 1.152928 32.17179 at 50iterations 0.6744849 14.78310 at 60iterations 0.3942012 9.152283 at 70iterations 0.2287068 4.299072 at 80iterations 0.1332403 2.648349 at 90iterations 7.7373132E-02 1.556005 at 100iterations 4.5102749E-02 0.9135206 at 110iterations 2.6180519E-02 0.5197403 at 120iterations 1.5150252E-02 0.3048401 at 130iterations 8.8069355E-03 0.1732597 at 140iterations 5.1073851E-03 0.1018925 at 150iterations 2.9679227E-03 5.5618286E-02 at 160iterations 1.7169575E-03 3.2978058E-02 at 170iterations 9.9865731E-04 1.7910004E-02 at 180iterations finished qdiffx linear iterations at : 12:12:56 total time elapsed so far: 15.07000 # loops : 180 mean,max change (kT/e) : 9.9865731E-04 1.7910004E-02 energy calculations done at 15.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.22000 DelPhi exited at 12:12:57 15.222u 0.343s 0:15.87 98.0% 0+0k 0+0io 0pf+0w