Sun Oct 9 08:49:34 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 Sun Oct 9 2011 at 08:49:34 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6037 !!! WARNING: HIR 702 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4798685 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): 3.860000 78.04700 ymin,ymax (A): 22.58000 84.26600 zmin,zma (A): 6.549000 68.81800 x,y,z range (A): 74.18700 61.68600 62.26900 scale (grids/A): 0.4798685 object centre (A): 40.95350 53.42300 37.68350 number of atom coordinates read : 6037 total number of charged atoms : 5869 net assigned charge : -0.9859477 assigned positive charge : 912.0580 centred at (gu) : 90.43269 89.24691 89.33734 assigned negative charge : -913.0518 centred at (gu) : 90.30689 89.23534 89.21653 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8583 nv = 96 ne = 84 npr = 121700 no. pairs analyzed = 121700 no. exposed pairs = 7550 no. arc points = 52045 no. surface atoms = 2517 nbur = 3520 mkacc time = 0.2100000 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 = 1.792000 m= 280 mr = 4387 m= 0 mr = 8 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4899 ## 833 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2494444E-10 7.8328649E-11 midg,1,midg; midg,igrid,midg -1.5229974E-11 5.3443920E-12 1,midg,midg; igrid,midg,midg -9.5321431E-11 1.1126764E-10 gauss-seidel spectral radius is 0.9778935 estimated iterations to convergence 56 setup time was (sec) 0.5800000 now iterating at: 08:49:34 rms-change max change #iterations 5.4443058E-02 9.967184 at 10iterations 2.6254395E-03 0.4848404 at 20iterations 1.5576938E-04 2.6191711E-02 at 30iterations 2.4266214E-05 4.8141479E-03 at 40iterations 6.5115819E-06 1.0499954E-03 at 50iterations finished qdiffx linear iterations at : 08:49:37 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 6.5115819E-06 1.0499954E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 08:49:38 3.597u 0.175s 0:04.04 93.0% 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 Sun Oct 9 2011 at 08:49:38 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6037 !!! WARNING: HIR 702 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.439605 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): 3.860000 78.04700 ymin,ymax (A): 22.58000 84.26600 zmin,zma (A): 6.549000 68.81800 x,y,z range (A): 74.18700 61.68600 62.26900 scale (grids/A): 1.439605 object centre (A): 40.95350 53.42300 37.68350 number of atom coordinates read : 6037 total number of charged atoms : 5869 net assigned charge : -0.9859477 assigned positive charge : 912.0580 centred at (gu) : 91.29629 87.73891 88.01063 assigned negative charge : -913.0518 centred at (gu) : 90.92039 87.70567 87.64948 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 98847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52045 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 25890 mr = 67446 m= 1711 mr = 16433 m= 20 mr = 590 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1084 time to turn everything in is 0.4800000 number of dielectric boundary points 41999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 842 ## 17 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 43011 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) : 0.4798685 object centre at (A) : 40.95350 53.42300 37.68350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3102649E-03 1.0499495E-02 midg,1,midg; midg,igrid,midg -1.4203312E-03 -2.3919567E-03 1,midg,midg; igrid,midg,midg -7.5309947E-03 1.3006659E-02 gauss-seidel spectral radius is 0.9979427 estimated iterations to convergence 175 setup time was (sec) 0.7000000 now iterating at: 08:49:39 rms-change max change #iterations 3.774890 169.3171 at 10iterations 1.483094 52.97060 at 20iterations 0.5848872 17.98588 at 30iterations 0.2312486 7.200626 at 40iterations 9.1248058E-02 2.746597 at 50iterations 3.6157962E-02 1.180235 at 60iterations 1.4271472E-02 0.5001526 at 70iterations 5.6817229E-03 0.1779642 at 80iterations 2.2641157E-03 7.5398207E-02 at 90iterations 9.0813107E-04 2.6782990E-02 at 100iterations 3.7173863E-04 1.2668610E-02 at 110iterations 1.5986165E-04 5.3710938E-03 at 120iterations finished qdiffx linear iterations at : 08:49:46 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.5986165E-04 5.3710938E-03 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 08:49:46 7.913u 0.197s 0:08.41 96.3% 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 Sun Oct 9 2011 at 08:49:46 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6037 !!! WARNING: HIR 702 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.159408 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): 3.860000 78.04700 ymin,ymax (A): 22.58000 84.26600 zmin,zma (A): 6.549000 68.81800 x,y,z range (A): 74.18700 61.68600 62.26900 scale (grids/A): 2.159408 object centre (A): 40.95350 53.42300 37.68350 number of atom coordinates read : 6037 total number of charged atoms : 5869 net assigned charge : -0.9859477 assigned positive charge : 912.0580 centred at (gu) : 91.94402 86.60811 87.01547 assigned negative charge : -913.0518 centred at (gu) : 91.38052 86.55830 86.47401 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 231220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52045 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 97698 mr = 166944 m= 20763 mr = 74665 m= 2085 mr = 14211 m= 63 mr = 1148 m= 0 mr = 10 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 3787 time to turn everything in is 1.150000 number of dielectric boundary points 94851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 46699 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) : 1.439605 object centre at (A) : 40.95350 53.42300 37.68350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1281391 0.1772728 midg,1,midg; midg,igrid,midg -1.6352156E-02 -2.8029298E-02 1,midg,midg; igrid,midg,midg -5.8245309E-02 0.1586202 gauss-seidel spectral radius is 0.9991403 estimated iterations to convergence 269 setup time was (sec) 1.390000 now iterating at: 08:49:48 rms-change max change #iterations 10.70620 291.5547 at 10iterations 6.111514 141.7897 at 20iterations 3.473394 71.85382 at 30iterations 1.960497 41.59261 at 40iterations 1.103944 21.75388 at 50iterations 0.6205203 12.89417 at 60iterations 0.3470297 7.991577 at 70iterations 0.1937712 3.823647 at 80iterations 0.1079078 2.222967 at 90iterations 6.0177799E-02 1.288567 at 100iterations 3.3415593E-02 0.7012024 at 110iterations 1.8568598E-02 0.3499141 at 120iterations 1.0301281E-02 0.1901989 at 130iterations 5.7249451E-03 0.1106932 at 140iterations 3.1744661E-03 5.3942680E-02 at 150iterations 1.7600049E-03 3.5633087E-02 at 160iterations 9.7663421E-04 1.7475128E-02 at 170iterations 5.4293551E-04 1.0554314E-02 at 180iterations finished qdiffx linear iterations at : 08:49:59 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 5.4293551E-04 1.0554314E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 08:50:00 13.052u 0.220s 0:13.56 97.8% 0+0k 0+0io 0pf+0w