Sat Oct 8 16:28:03 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 8 2011 at 16:28:03 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 = 2287 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6473787 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): 25.01400 74.48000 ymin,ymax (A): -16.03400 29.72200 zmin,zma (A): -18.72700 36.26400 x,y,z range (A): 49.46600 45.75600 54.99100 scale (grids/A): 0.6473787 object centre (A): 49.74700 6.844000 8.768500 number of atom coordinates read : 2287 total number of charged atoms : 2190 net assigned charge : 5.000005 assigned positive charge : 334.9793 centred at (gu) : 90.14410 88.58444 89.85966 assigned negative charge : -329.9799 centred at (gu) : 90.22657 88.68984 89.85882 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6420 nv = 96 ne = 84 npr = 46962 no. pairs analyzed = 46962 no. exposed pairs = 2754 no. arc points = 19200 no. surface atoms = 946 nbur = 1341 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3605 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1919 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7753 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9344425E-09 8.6359249E-09 midg,1,midg; midg,igrid,midg 2.8892702E-08 -2.9118290E-09 1,midg,midg; igrid,midg,midg 1.8103362E-08 -1.3247322E-09 gauss-seidel spectral radius is 0.9876075 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 16:28:04 rms-change max change #iterations 0.1398944 22.53065 at 10iterations 1.4325579E-02 2.000227 at 20iterations 1.4990802E-03 0.2261314 at 30iterations 1.8377769E-04 3.1235695E-02 at 40iterations 3.1827643E-05 5.8116913E-03 at 50iterations finished qdiffx linear iterations at : 16:28:07 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 3.1827643E-05 5.8116913E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 16:28:08 4.195u 0.273s 0:04.76 93.6% 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 8 2011 at 16:28:08 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 = 2287 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.942136 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): 25.01400 74.48000 ymin,ymax (A): -16.03400 29.72200 zmin,zma (A): -18.72700 36.26400 x,y,z range (A): 49.46600 45.75600 54.99100 scale (grids/A): 1.942136 object centre (A): 49.74700 6.844000 8.768500 number of atom coordinates read : 2287 total number of charged atoms : 2190 net assigned charge : 5.000005 assigned positive charge : 334.9793 centred at (gu) : 90.43193 85.75309 89.57876 assigned negative charge : -329.9799 centred at (gu) : 90.67956 86.06936 89.57620 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19200 grid for indexing accessible points = 1.400000 m= 25478 mr = 49330 m= 4265 mr = 19022 m= 232 mr = 2756 m= 9 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 844 time to turn everything in is 0.6300000 number of dielectric boundary points 28615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17253 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) : 0.6473787 object centre at (A) : 49.74700 6.844000 8.768500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9868308E-02 1.4849917E-02 midg,1,midg; midg,igrid,midg 2.3424638E-02 -3.0365814E-03 1,midg,midg; igrid,midg,midg 1.4329566E-02 -4.1110784E-02 gauss-seidel spectral radius is 0.9986507 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 16:28:09 rms-change max change #iterations 4.053850 184.9340 at 10iterations 1.897526 67.88664 at 20iterations 0.8917766 29.98956 at 30iterations 0.4209665 13.73270 at 40iterations 0.1971585 6.403071 at 50iterations 9.3171388E-02 3.078451 at 60iterations 4.3843433E-02 1.417999 at 70iterations 2.0604199E-02 0.7876225 at 80iterations 9.7433412E-03 0.3180943 at 90iterations 4.6074032E-03 0.1546650 at 100iterations 2.1705772E-03 6.9620132E-02 at 110iterations 1.0236872E-03 3.2773018E-02 at 120iterations finished qdiffx linear iterations at : 16:28:18 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 1.0236872E-03 3.2773018E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 16:28:18 9.725u 0.344s 0:10.38 96.9% 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 8 2011 at 16:28:18 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 = 2287 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.913204 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): 25.01400 74.48000 ymin,ymax (A): -16.03400 29.72200 zmin,zma (A): -18.72700 36.26400 x,y,z range (A): 49.46600 45.75600 54.99100 scale (grids/A): 2.913204 object centre (A): 49.74700 6.844000 8.768500 number of atom coordinates read : 2287 total number of charged atoms : 2190 net assigned charge : 5.000005 assigned positive charge : 334.9793 centred at (gu) : 90.64763 83.62939 89.36806 assigned negative charge : -329.9799 centred at (gu) : 91.01947 84.10398 89.36431 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 161486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19200 grid for indexing accessible points = 1.400000 m= 81778 mr = 119064 m= 30431 mr = 67539 m= 7801 mr = 24763 m= 1048 mr = 6064 m= 56 mr = 682 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2742 time to turn everything in is 1.620000 number of dielectric boundary points 64474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 17520 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) : 1.942136 object centre at (A) : 49.74700 6.844000 8.768500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2981775 9.5828101E-02 midg,1,midg; midg,igrid,midg 0.1478830 -4.5821790E-02 1,midg,midg; igrid,midg,midg 9.7109847E-02 -0.5443479 gauss-seidel spectral radius is 0.9992544 estimated iterations to convergence 289 setup time was (sec) 1.950000 now iterating at: 16:28:21 rms-change max change #iterations 9.328798 392.4205 at 10iterations 5.449044 132.9578 at 20iterations 3.155502 63.38711 at 30iterations 1.831880 47.78921 at 40iterations 1.061266 23.68600 at 50iterations 0.6126650 13.97171 at 60iterations 0.3537694 6.532613 at 70iterations 0.2035045 4.104303 at 80iterations 0.1175142 2.115757 at 90iterations 6.7555957E-02 1.208527 at 100iterations 3.8836148E-02 0.7311125 at 110iterations 2.2338619E-02 0.4165878 at 120iterations 1.2853001E-02 0.2631855 at 130iterations 7.3785172E-03 0.1325889 at 140iterations 4.2536645E-03 7.2022438E-02 at 150iterations 2.4563270E-03 4.4667006E-02 at 160iterations 1.4232943E-03 2.6803017E-02 at 170iterations 8.3282625E-04 1.5563011E-02 at 180iterations finished qdiffx linear iterations at : 16:28:35 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 8.3282625E-04 1.5563011E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.29000 DelPhi exited at 16:28:35 16.290u 0.341s 0:16.92 98.2% 0+0k 0+0io 0pf+0w