Sat Oct 15 10:22:37 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 Sat Oct 15 2011 at 10:22:37 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2720 !!! WARNING: HIR 136 has a net charge of 0.5140 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: 0.5663559 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): -21.87700 33.04400 ymin,ymax (A): -21.38000 26.25200 zmin,zma (A): 2.428000 65.28600 x,y,z range (A): 54.92100 47.63200 62.85800 scale (grids/A): 0.5663559 object centre (A): 5.583499 2.436001 33.85700 number of atom coordinates read : 2720 total number of charged atoms : 2569 net assigned charge : 1.4009103E-02 assigned positive charge : 401.5894 centred at (gu) : 89.69711 90.78619 92.65191 assigned negative charge : -401.5762 centred at (gu) : 89.60746 90.79008 92.58714 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5661 nv = 96 ne = 84 npr = 54607 no. pairs analyzed = 54607 no. exposed pairs = 3627 no. arc points = 25622 no. surface atoms = 1230 nbur = 1490 mkacc time = 0.1700000 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= 218 mr = 2733 m= 0 mr = 5 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2641 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3762180E-10 1.5031921E-09 midg,1,midg; midg,igrid,midg 2.5726870E-11 -7.9247865E-11 1,midg,midg; igrid,midg,midg -1.2286959E-09 1.0057910E-09 gauss-seidel spectral radius is 0.9838999 estimated iterations to convergence 65 setup time was (sec) 0.7300000 now iterating at: 10:22:38 rms-change max change #iterations 8.3028264E-02 14.76891 at 10iterations 6.1354926E-03 1.047443 at 20iterations 4.4969306E-04 7.3002815E-02 at 30iterations 3.3610944E-05 5.8593750E-03 at 40iterations 2.7170561E-06 4.4631958E-04 at 50iterations finished qdiffx linear iterations at : 10:22:42 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 2.7170561E-06 4.4631958E-04 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.020000 DelPhi exited at 10:22:43 5.021u 0.407s 0:06.07 89.2% 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 Sat Oct 15 2011 at 10:22:43 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2720 !!! WARNING: HIR 136 has a net charge of 0.5140 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: 1.699068 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): -21.87700 33.04400 ymin,ymax (A): -21.38000 26.25200 zmin,zma (A): 2.428000 65.28600 x,y,z range (A): 54.92100 47.63200 62.85800 scale (grids/A): 1.699068 object centre (A): 5.583499 2.436001 33.85700 number of atom coordinates read : 2720 total number of charged atoms : 2569 net assigned charge : 1.4009103E-02 assigned positive charge : 401.5894 centred at (gu) : 89.09066 92.35773 97.95496 assigned negative charge : -401.5762 centred at (gu) : 88.82209 92.37003 97.76110 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 62177 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25622 grid for indexing accessible points = 1.400000 m= 18282 mr = 40348 m= 1947 mr = 12100 m= 43 mr = 901 m= 0 mr = 4 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 29096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 253 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 19844 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) : 0.5663559 object centre at (A) : 5.583499 2.436001 33.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9642316E-02 3.2879107E-02 midg,1,midg; midg,igrid,midg -5.7307514E-04 -4.9036276E-03 1,midg,midg; igrid,midg,midg -2.6170400E-03 8.8339252E-03 gauss-seidel spectral radius is 0.9983018 estimated iterations to convergence 193 setup time was (sec) 0.9900000 now iterating at: 10:22:45 rms-change max change #iterations 3.417719 153.2274 at 10iterations 1.452665 58.17993 at 20iterations 0.6208919 25.40396 at 30iterations 0.2664613 10.61124 at 40iterations 0.1137908 4.184914 at 50iterations 4.8753776E-02 1.794655 at 60iterations 2.0895775E-02 0.8788117 at 70iterations 8.9404834E-03 0.3126841 at 80iterations 3.8539376E-03 0.1412838 at 90iterations 1.6422403E-03 6.9411278E-02 at 100iterations 7.0692552E-04 2.7122498E-02 at 110iterations 3.0238734E-04 1.0887146E-02 at 120iterations finished qdiffx linear iterations at : 10:22:56 total time elapsed so far: 11.76000 # loops : 120 mean,max change (kT/e) : 3.0238734E-04 1.0887146E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 10:22:56 11.989u 0.481s 0:13.11 95.0% 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 10:22:56 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2720 !!! WARNING: HIR 136 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.548602 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): -21.87700 33.04400 ymin,ymax (A): -21.38000 26.25200 zmin,zma (A): 2.428000 65.28600 x,y,z range (A): 54.92100 47.63200 62.85800 scale (grids/A): 2.548602 object centre (A): 5.583499 2.436001 33.85700 number of atom coordinates read : 2720 total number of charged atoms : 2569 net assigned charge : 1.4009103E-02 assigned positive charge : 401.5894 centred at (gu) : 88.63572 93.53644 101.9323 assigned negative charge : -401.5762 centred at (gu) : 88.23302 93.55501 101.6415 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 144546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25622 grid for indexing accessible points = 1.400000 m= 62857 mr = 99386 m= 18066 mr = 48569 m= 3038 mr = 13051 m= 217 mr = 1974 m= 6 mr = 92 m= 0 mr = 2 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 65656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 20527 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) : 1.699068 object centre at (A) : 5.583499 2.436001 33.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5199769 0.5184985 midg,1,midg; midg,igrid,midg 7.4142381E-03 -9.0990469E-02 1,midg,midg; igrid,midg,midg -6.4391635E-02 0.1007000 gauss-seidel spectral radius is 0.9991692 estimated iterations to convergence 274 setup time was (sec) 1.970000 now iterating at: 10:22:59 rms-change max change #iterations 8.643669 307.8578 at 10iterations 4.885822 124.1828 at 20iterations 2.744423 60.96735 at 30iterations 1.538672 34.57014 at 40iterations 0.8604140 19.42863 at 50iterations 0.4797198 10.70257 at 60iterations 0.2672522 5.756776 at 70iterations 0.1487583 3.318520 at 80iterations 8.2777962E-02 1.774526 at 90iterations 4.5961138E-02 0.9614711 at 100iterations 2.5536293E-02 0.5406895 at 110iterations 1.4161951E-02 0.3143616 at 120iterations 7.8736013E-03 0.2143097 at 130iterations 4.3669660E-03 9.0911865E-02 at 140iterations 2.4304600E-03 5.0416946E-02 at 150iterations 1.3462778E-03 2.9703140E-02 at 160iterations 7.4919849E-04 1.4942169E-02 at 170iterations 4.1639555E-04 8.3694458E-03 at 180iterations finished qdiffx linear iterations at : 10:23:16 total time elapsed so far: 19.10000 # loops : 180 mean,max change (kT/e) : 4.1639555E-04 8.3694458E-03 energy calculations done at 19.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.30000 DelPhi exited at 10:23:17 19.302u 0.514s 0:20.37 97.2% 0+0k 0+0io 0pf+0w