Mon Oct 10 20:16:35 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 Mon Oct 10 2011 at 20:16:35 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 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: 0.6153952 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): -10.43000 40.31400 ymin,ymax (A): 33.39800 88.76300 zmin,zma (A): -12.35300 45.49600 x,y,z range (A): 50.74400 55.36500 57.84900 scale (grids/A): 0.6153952 object centre (A): 14.94200 61.08050 16.57150 number of atom coordinates read : 2578 total number of charged atoms : 2442 net assigned charge : -0.9999937 assigned positive charge : 381.4088 centred at (gu) : 90.62602 88.22411 90.08199 assigned negative charge : -382.4099 centred at (gu) : 90.58308 88.36347 90.08743 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6629 nv = 96 ne = 84 npr = 51235 no. pairs analyzed = 51235 no. exposed pairs = 3632 no. arc points = 25662 no. surface atoms = 1200 nbur = 1378 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3238 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2800000 number of dielectric boundary points 3721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2540 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4583871E-10 -1.1976445E-09 midg,1,midg; midg,igrid,midg 1.0470512E-08 -6.0217138E-09 1,midg,midg; igrid,midg,midg -2.8954010E-09 1.8197420E-09 gauss-seidel spectral radius is 0.9863380 estimated iterations to convergence 70 setup time was (sec) 0.5000000 now iterating at: 20:16:36 rms-change max change #iterations 0.1152963 19.07737 at 10iterations 1.0482943E-02 1.734100 at 20iterations 9.4835210E-04 0.1475220 at 30iterations 9.5073774E-05 1.8878937E-02 at 40iterations 1.2599987E-05 2.2583008E-03 at 50iterations finished qdiffx linear iterations at : 20:16:38 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 1.2599987E-05 2.2583008E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 20:16:39 3.126u 0.138s 0:03.67 88.5% 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 Mon Oct 10 2011 at 20:16:39 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 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: 1.846186 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): -10.43000 40.31400 ymin,ymax (A): 33.39800 88.76300 zmin,zma (A): -12.35300 45.49600 x,y,z range (A): 50.74400 55.36500 57.84900 scale (grids/A): 1.846186 object centre (A): 14.94200 61.08050 16.57150 number of atom coordinates read : 2578 total number of charged atoms : 2442 net assigned charge : -0.9999937 assigned positive charge : 381.4088 centred at (gu) : 91.87746 84.67125 90.24516 assigned negative charge : -382.4099 centred at (gu) : 91.74937 85.09059 90.26225 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25662 grid for indexing accessible points = 1.400000 m= 24592 mr = 45732 m= 4015 mr = 17123 m= 197 mr = 2213 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 396 time to turn everything in is 0.5000000 number of dielectric boundary points 34210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19154 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) : 0.6153952 object centre at (A) : 14.94200 61.08050 16.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6444283E-03 -3.3863313E-02 midg,1,midg; midg,igrid,midg 5.5722550E-02 -1.2770114E-02 1,midg,midg; igrid,midg,midg -2.4830108E-03 -6.1365915E-03 gauss-seidel spectral radius is 0.9985660 estimated iterations to convergence 209 setup time was (sec) 0.7600000 now iterating at: 20:16:40 rms-change max change #iterations 3.905275 160.5861 at 10iterations 1.780915 79.73357 at 20iterations 0.8140290 27.18829 at 30iterations 0.3736105 12.97806 at 40iterations 0.1709910 5.666615 at 50iterations 7.8537591E-02 2.504456 at 60iterations 3.6038939E-02 1.203865 at 70iterations 1.6445894E-02 0.5999432 at 80iterations 7.5521320E-03 0.2533722 at 90iterations 3.4821578E-03 0.1134449 at 100iterations 1.5979112E-03 6.1195374E-02 at 110iterations 7.3794287E-04 2.5729179E-02 at 120iterations finished qdiffx linear iterations at : 20:16:46 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 7.3794287E-04 2.5729179E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.850000 DelPhi exited at 20:16:47 6.853u 0.184s 0:07.40 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 Mon Oct 10 2011 at 20:16:47 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2578 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: 2.769279 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): -10.43000 40.31400 ymin,ymax (A): 33.39800 88.76300 zmin,zma (A): -12.35300 45.49600 x,y,z range (A): 50.74400 55.36500 57.84900 scale (grids/A): 2.769279 object centre (A): 14.94200 61.08050 16.57150 number of atom coordinates read : 2578 total number of charged atoms : 2442 net assigned charge : -0.9999937 assigned positive charge : 381.4088 centred at (gu) : 92.81609 82.00681 90.36758 assigned negative charge : -382.4099 centred at (gu) : 92.62397 82.63589 90.39340 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 162479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25662 grid for indexing accessible points = 1.400000 m= 78433 mr = 111364 m= 29086 mr = 61453 m= 6998 mr = 22517 m= 885 mr = 4894 m= 30 mr = 504 m= 0 mr = 11 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 1292 time to turn everything in is 1.260000 number of dielectric boundary points 77168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 19532 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) : 1.846186 object centre at (A) : 14.94200 61.08050 16.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0476327E-02 -0.3815437 midg,1,midg; midg,igrid,midg 0.8693785 -0.2424561 1,midg,midg; igrid,midg,midg 3.1535886E-02 -0.1102657 gauss-seidel spectral radius is 0.9992501 estimated iterations to convergence 288 setup time was (sec) 1.530000 now iterating at: 20:16:48 rms-change max change #iterations 9.613009 348.9626 at 10iterations 5.683973 139.3632 at 20iterations 3.317718 76.71750 at 30iterations 1.930941 42.15664 at 40iterations 1.118515 23.14675 at 50iterations 0.6454161 13.27814 at 60iterations 0.3727565 8.705788 at 70iterations 0.2147784 4.472885 at 80iterations 0.1231283 2.392420 at 90iterations 7.0836104E-02 1.540480 at 100iterations 4.0622741E-02 0.8252506 at 110iterations 2.3339812E-02 0.4267902 at 120iterations 1.3398681E-02 0.2676306 at 130iterations 7.6770848E-03 0.1413383 at 140iterations 4.4097900E-03 8.7618828E-02 at 150iterations 2.5391355E-03 5.0397873E-02 at 160iterations 1.4708627E-03 3.1093597E-02 at 170iterations 8.5434970E-04 1.6616821E-02 at 180iterations finished qdiffx linear iterations at : 20:16:58 total time elapsed so far: 11.10000 # loops : 180 mean,max change (kT/e) : 8.5434970E-04 1.6616821E-02 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 20:16:59 11.298u 0.189s 0:12.06 95.1% 0+0k 0+0io 0pf+0w