Tue Oct 11 03:41:39 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 Tue Oct 11 2011 at 03:41:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 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: 0.5086732 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): -31.49500 23.12500 ymin,ymax (A): -8.281000 47.20200 zmin,zma (A): 42.79900 112.7850 x,y,z range (A): 54.62000 55.48300 69.98599 scale (grids/A): 0.5086732 object centre (A): -4.184999 19.46050 77.79200 number of atom coordinates read : 3591 total number of charged atoms : 3435 net assigned charge : 12.00004 assigned positive charge : 553.1312 centred at (gu) : 90.49592 89.65257 92.12786 assigned negative charge : -541.1327 centred at (gu) : 90.66685 89.86626 92.29828 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5830 nv = 96 ne = 84 npr = 70527 no. pairs analyzed = 70527 no. exposed pairs = 4766 no. arc points = 33838 no. surface atoms = 1574 nbur = 2017 mkacc time = 0.1900000 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 = 1.680000 m= 208 mr = 2812 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3318 ## 556 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7895 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6566480E-10 -2.7384159E-10 midg,1,midg; midg,igrid,midg 5.8875399E-10 -2.1005137E-10 1,midg,midg; igrid,midg,midg 4.0706100E-10 -1.7289124E-10 gauss-seidel spectral radius is 0.9801514 estimated iterations to convergence 59 setup time was (sec) 0.6800000 now iterating at: 03:41:40 rms-change max change #iterations 5.7856403E-02 9.415773 at 10iterations 3.2153158E-03 0.6146507 at 20iterations 2.2370335E-04 3.5926819E-02 at 30iterations 3.1527921E-05 6.0310364E-03 at 40iterations 7.1271834E-06 1.4925003E-03 at 50iterations finished qdiffx linear iterations at : 03:41:44 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 7.1271834E-06 1.4925003E-03 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.780000 DelPhi exited at 03:41:45 4.788u 0.430s 0:05.93 87.8% 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 Tue Oct 11 2011 at 03:41:45 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 = 3591 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: 1.526020 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): -31.49500 23.12500 ymin,ymax (A): -8.281000 47.20200 zmin,zma (A): 42.79900 112.7850 x,y,z range (A): 54.62000 55.48300 69.98599 scale (grids/A): 1.526020 object centre (A): -4.184999 19.46050 77.79200 number of atom coordinates read : 3591 total number of charged atoms : 3435 net assigned charge : 12.00004 assigned positive charge : 553.1312 centred at (gu) : 91.48675 88.95679 96.38290 assigned negative charge : -541.1327 centred at (gu) : 91.99998 89.59835 96.89480 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33838 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19154 mr = 42026 m= 1699 mr = 12635 m= 33 mr = 647 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1286 time to turn everything in is 0.5600000 number of dielectric boundary points 30142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 512 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25738 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) : 0.5086732 object centre at (A) : -4.184999 19.46050 77.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5696783E-03 -1.7187741E-02 midg,1,midg; midg,igrid,midg 1.9562701E-02 -6.7415256E-03 1,midg,midg; igrid,midg,midg 1.7463192E-02 3.2497821E-03 gauss-seidel spectral radius is 0.9979712 estimated iterations to convergence 177 setup time was (sec) 0.8600000 now iterating at: 03:41:46 rms-change max change #iterations 3.164140 154.2054 at 10iterations 1.252272 49.12010 at 20iterations 0.4961673 20.68509 at 30iterations 0.1967032 6.864471 at 40iterations 7.7822119E-02 2.700544 at 50iterations 3.0947506E-02 1.153370 at 60iterations 1.2312602E-02 0.4524593 at 70iterations 4.8895688E-03 0.2094803 at 80iterations 1.9453929E-03 7.1770668E-02 at 90iterations 7.7548600E-04 2.6749611E-02 at 100iterations 3.0951406E-04 1.1619568E-02 at 110iterations 1.2561043E-04 4.9018860E-03 at 120iterations finished qdiffx linear iterations at : 03:41:56 total time elapsed so far: 10.81000 # loops : 120 mean,max change (kT/e) : 1.2561043E-04 4.9018860E-03 energy calculations done at 10.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 03:41:57 10.967u 0.476s 0:12.20 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 Tue Oct 11 2011 at 03:41:57 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 = 3591 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: 2.289030 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): -31.49500 23.12500 ymin,ymax (A): -8.281000 47.20200 zmin,zma (A): 42.79900 112.7850 x,y,z range (A): 54.62000 55.48300 69.98599 scale (grids/A): 2.289030 object centre (A): -4.184999 19.46050 77.79200 number of atom coordinates read : 3591 total number of charged atoms : 3435 net assigned charge : 12.00004 assigned positive charge : 553.1312 centred at (gu) : 92.22986 88.43483 99.57401 assigned negative charge : -541.1327 centred at (gu) : 92.99994 89.39740 100.3422 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 149826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33838 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 66995 mr = 103127 m= 17668 mr = 51595 m= 2384 mr = 12816 m= 91 mr = 1298 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 4325 time to turn everything in is 1.330000 number of dielectric boundary points 68123 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 27411 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) : 1.526020 object centre at (A) : -4.184999 19.46050 77.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1553580 -0.4516881 midg,1,midg; midg,igrid,midg 0.3254410 -0.1204518 1,midg,midg; igrid,midg,midg 0.2945165 5.7745080E-02 gauss-seidel spectral radius is 0.9990855 estimated iterations to convergence 261 setup time was (sec) 1.680000 now iterating at: 03:41:59 rms-change max change #iterations 8.707502 294.1094 at 10iterations 4.900615 128.2916 at 20iterations 2.719597 108.7066 at 30iterations 1.500353 38.72781 at 40iterations 0.8244691 20.58146 at 50iterations 0.4521787 12.08848 at 60iterations 0.2465107 5.655029 at 70iterations 0.1343822 3.349265 at 80iterations 7.3144346E-02 1.703674 at 90iterations 3.9683118E-02 0.9303665 at 100iterations 2.1488488E-02 0.4678268 at 110iterations 1.1665410E-02 0.2388630 at 120iterations 6.3180802E-03 0.1373482 at 130iterations 3.4187681E-03 7.3978424E-02 at 140iterations 1.8478356E-03 4.0900946E-02 at 150iterations 9.9971704E-04 2.1759033E-02 at 160iterations 5.3932407E-04 1.0993958E-02 at 170iterations 2.9207015E-04 6.1035156E-03 at 180iterations finished qdiffx linear iterations at : 03:42:15 total time elapsed so far: 18.08000 # loops : 180 mean,max change (kT/e) : 2.9207015E-04 6.1035156E-03 energy calculations done at 18.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.24000 DelPhi exited at 03:42:17 18.245u 0.494s 0:19.71 95.0% 0+0k 0+0io 0pf+0w