Mon Oct 10 14:05:43 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 14:05:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5339 !!! WARNING: ASN 273 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5004358 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): 9.144000 74.62900 ymin,ymax (A): -30.52500 36.62200 zmin,zma (A): -7.101000 64.03700 x,y,z range (A): 65.48500 67.14700 71.13800 scale (grids/A): 0.5004358 object centre (A): 41.88650 3.048501 28.46800 number of atom coordinates read : 5339 total number of charged atoms : 5167 net assigned charge : -0.7719558 assigned positive charge : 823.0614 centred at (gu) : 89.46969 89.06768 89.19826 assigned negative charge : -823.8392 centred at (gu) : 89.38615 89.00430 89.28574 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8350 nv = 96 ne = 84 npr = 106392 no. pairs analyzed = 106392 no. exposed pairs = 6829 no. arc points = 46271 no. surface atoms = 2297 nbur = 3042 mkacc time = 0.2500000 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 = 1.708000 m= 304 mr = 4328 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4447 ## 664 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9906855E-10 -1.4147357E-10 midg,1,midg; midg,igrid,midg -1.6600128E-10 8.8853799E-11 1,midg,midg; igrid,midg,midg -1.9424790E-10 1.3188198E-10 gauss-seidel spectral radius is 0.9796220 estimated iterations to convergence 58 setup time was (sec) 0.7700000 now iterating at: 14:05:44 rms-change max change #iterations 6.6583671E-02 11.25911 at 10iterations 5.0072223E-03 0.9150276 at 20iterations 1.6352921E-03 0.2451134 at 30iterations 7.5644662E-04 0.1101322 at 40iterations 3.6402085E-04 4.8851013E-02 at 50iterations finished qdiffx linear iterations at : 14:05:46 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 3.6402085E-04 4.8851013E-02 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 14:05:47 3.783u 0.226s 0:04.35 91.9% 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 Mon Oct 10 2011 at 14:05:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5339 !!! WARNING: ASN 273 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.501307 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): 9.144000 74.62900 ymin,ymax (A): -30.52500 36.62200 zmin,zma (A): -7.101000 64.03700 x,y,z range (A): 65.48500 67.14700 71.13800 scale (grids/A): 1.501307 object centre (A): 41.88650 3.048501 28.46800 number of atom coordinates read : 5339 total number of charged atoms : 5167 net assigned charge : -0.7719558 assigned positive charge : 823.0614 centred at (gu) : 88.40768 87.20189 87.59328 assigned negative charge : -823.8392 centred at (gu) : 88.15860 87.01246 87.85760 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 94190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46271 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 29302 mr = 64456 m= 2599 mr = 20143 m= 36 mr = 1157 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 90 time to turn everything in is 0.7100000 number of dielectric boundary points 40371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 518 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 38531 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) : 0.5004358 object centre at (A) : 41.88650 3.048501 28.46800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7819748E-03 -1.6210770E-02 midg,1,midg; midg,igrid,midg -1.9213530E-03 1.2105316E-02 1,midg,midg; igrid,midg,midg -1.0919158E-03 2.0715268E-04 gauss-seidel spectral radius is 0.9980853 estimated iterations to convergence 182 setup time was (sec) 0.9900000 now iterating at: 14:05:48 rms-change max change #iterations 3.959390 175.6925 at 10iterations 1.603296 59.96720 at 20iterations 0.6510310 21.64644 at 30iterations 0.2656212 9.169418 at 40iterations 0.1087837 3.369419 at 50iterations 4.4399627E-02 1.415606 at 60iterations 1.8413434E-02 0.5488281 at 70iterations 7.9266261E-03 0.2650871 at 80iterations 3.7162784E-03 0.1229858 at 90iterations 2.0249118E-03 6.1586380E-02 at 100iterations 1.3120868E-03 4.1549683E-02 at 110iterations 9.4092399E-04 2.7475357E-02 at 120iterations finished qdiffx linear iterations at : 14:05:55 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 9.4092399E-04 2.7475357E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:05:55 7.783u 0.170s 0:08.33 95.4% 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 14:05:55 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 = 5339 !!! WARNING: ASN 273 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.251961 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): 9.144000 74.62900 ymin,ymax (A): -30.52500 36.62200 zmin,zma (A): -7.101000 64.03700 x,y,z range (A): 65.48500 67.14700 71.13800 scale (grids/A): 2.251961 object centre (A): 41.88650 3.048501 28.46800 number of atom coordinates read : 5339 total number of charged atoms : 5167 net assigned charge : -0.7719558 assigned positive charge : 823.0614 centred at (gu) : 87.61099 85.80270 86.38961 assigned negative charge : -823.8392 centred at (gu) : 87.23779 85.51861 86.78641 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 219199 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46271 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 102170 mr = 158086 m= 27845 mr = 80579 m= 3648 mr = 20903 m= 160 mr = 2274 m= 0 mr = 27 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 302 time to turn everything in is 1.740000 number of dielectric boundary points 91153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 41163 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) : 1.501307 object centre at (A) : 41.88650 3.048501 28.46800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9695044E-02 -0.3344895 midg,1,midg; midg,igrid,midg 1.0622789E-03 0.1408941 1,midg,midg; igrid,midg,midg 5.3116968E-03 9.8091108E-04 gauss-seidel spectral radius is 0.9991723 estimated iterations to convergence 274 setup time was (sec) 2.090000 now iterating at: 14:05:58 rms-change max change #iterations 10.94711 285.5532 at 10iterations 6.328616 144.8521 at 20iterations 3.628943 86.94073 at 30iterations 2.066779 43.43095 at 40iterations 1.171996 24.37347 at 50iterations 0.6616620 13.75628 at 60iterations 0.3717217 6.796430 at 70iterations 0.2097569 3.540551 at 80iterations 0.1175907 2.127662 at 90iterations 6.6020861E-02 1.207403 at 100iterations 3.6938548E-02 0.6985435 at 110iterations 2.0755485E-02 0.3816094 at 120iterations 1.1710359E-02 0.2216911 at 130iterations 6.6588297E-03 0.1192207 at 140iterations 3.8477804E-03 6.9583893E-02 at 150iterations 2.3124153E-03 5.1096916E-02 at 160iterations 1.4779015E-03 2.6622772E-02 at 170iterations 1.0201172E-03 1.8602371E-02 at 180iterations finished qdiffx linear iterations at : 14:06:09 total time elapsed so far: 13.86000 # loops : 180 mean,max change (kT/e) : 1.0201172E-03 1.8602371E-02 energy calculations done at 13.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.05000 DelPhi exited at 14:06:10 14.049u 0.246s 0:14.73 96.9% 0+0k 0+0io 0pf+0w