Mon Oct 10 13:59:25 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 Mon Oct 10 2011 at 13:59:25 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2612 !!! WARNING: SER 2 has a net charge of 0.5000 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6170164 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): -31.35700 17.54200 ymin,ymax (A): -23.56900 22.60500 zmin,zma (A): -12.47800 45.21900 x,y,z range (A): 48.89900 46.17400 57.69700 scale (grids/A): 0.6170164 object centre (A): -6.907500 -0.4820004 16.37050 number of atom coordinates read : 2612 total number of charged atoms : 2468 net assigned charge : 4.448013 assigned positive charge : 397.3310 centred at (gu) : 88.59235 89.33183 89.54700 assigned negative charge : -392.8835 centred at (gu) : 88.46225 89.37606 89.43783 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6381 nv = 96 ne = 84 npr = 55147 no. pairs analyzed = 55147 no. exposed pairs = 2978 no. arc points = 21408 no. surface atoms = 1006 nbur = 1606 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 3510 m= 0 mr = 33 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.3000000 number of dielectric boundary points 3129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2214 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7731014E-09 9.0850536E-09 midg,1,midg; midg,igrid,midg 7.0857142E-09 6.0385308E-10 1,midg,midg; igrid,midg,midg -6.5663603E-09 8.2850162E-09 gauss-seidel spectral radius is 0.9863935 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 13:59:26 rms-change max change #iterations 0.1273819 22.57380 at 10iterations 1.1488575E-02 1.641769 at 20iterations 1.0641695E-03 0.1660385 at 30iterations 9.7789816E-05 1.5294075E-02 at 40iterations 8.9210444E-06 1.3618469E-03 at 50iterations finished qdiffx linear iterations at : 13:59:30 total time elapsed so far: 5.070000 # loops : 50 mean,max change (kT/e) : 8.9210444E-06 1.3618469E-03 energy calculations done at 5.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 13:59:31 5.246u 0.407s 0:06.41 87.9% 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 13:59:31 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2612 !!! WARNING: SER 2 has a net charge of 0.5000 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.851049 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): -31.35700 17.54200 ymin,ymax (A): -23.56900 22.60500 zmin,zma (A): -12.47800 45.21900 x,y,z range (A): 48.89900 46.17400 57.69700 scale (grids/A): 1.851049 object centre (A): -6.907500 -0.4820004 16.37050 number of atom coordinates read : 2612 total number of charged atoms : 2468 net assigned charge : 4.448013 assigned positive charge : 397.3310 centred at (gu) : 85.77648 87.99516 88.64037 assigned negative charge : -392.8835 centred at (gu) : 85.38654 88.12801 88.31322 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21408 grid for indexing accessible points = 1.400000 m= 23400 mr = 48923 m= 3144 mr = 17223 m= 143 mr = 1897 m= 0 mr = 41 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 4905 time to turn everything in is 0.5600000 number of dielectric boundary points 28571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19353 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) : 0.6170164 object centre at (A) : -6.907500 -0.4820004 16.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2648693E-02 2.5932463E-02 midg,1,midg; midg,igrid,midg 1.0892034E-02 2.5302386E-03 1,midg,midg; igrid,midg,midg -2.8125902E-03 3.9613564E-02 gauss-seidel spectral radius is 0.9985527 estimated iterations to convergence 208 setup time was (sec) 0.8900000 now iterating at: 13:59:32 rms-change max change #iterations 4.027735 160.0475 at 10iterations 1.848081 66.24545 at 20iterations 0.8450340 28.30439 at 30iterations 0.3870117 13.96649 at 40iterations 0.1779099 6.037804 at 50iterations 8.1230097E-02 2.589336 at 60iterations 3.7330519E-02 1.219604 at 70iterations 1.7060345E-02 0.5322132 at 80iterations 7.8418432E-03 0.2397876 at 90iterations 3.5841800E-03 0.1155488 at 100iterations 1.6369746E-03 5.1258087E-02 at 110iterations 7.5433368E-04 2.6592255E-02 at 120iterations finished qdiffx linear iterations at : 13:59:44 total time elapsed so far: 12.57000 # loops : 120 mean,max change (kT/e) : 7.5433368E-04 2.6592255E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 13:59:45 12.741u 0.462s 0:13.69 96.4% 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 13:59:46 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2612 !!! WARNING: SER 2 has a net charge of 0.5000 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.776574 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): -31.35700 17.54200 ymin,ymax (A): -23.56900 22.60500 zmin,zma (A): -12.47800 45.21900 x,y,z range (A): 48.89900 46.17400 57.69700 scale (grids/A): 2.776574 object centre (A): -6.907500 -0.4820004 16.37050 number of atom coordinates read : 2612 total number of charged atoms : 2468 net assigned charge : 4.448013 assigned positive charge : 397.3310 centred at (gu) : 83.66452 86.99252 87.96042 assigned negative charge : -392.8835 centred at (gu) : 83.07973 87.19195 87.46976 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 162330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21408 grid for indexing accessible points = 1.400000 m= 78601 mr = 118611 m= 25538 mr = 64584 m= 5415 mr = 20464 m= 652 mr = 4076 m= 21 mr = 434 m= 0 mr = 5 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 17295 time to turn everything in is 1.430000 number of dielectric boundary points 64383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 19741 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) : 1.851049 object centre at (A) : -6.907500 -0.4820004 16.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4114266E-02 0.3382690 midg,1,midg; midg,igrid,midg 0.1326576 1.6685486E-02 1,midg,midg; igrid,midg,midg -1.9704260E-02 0.5382339 gauss-seidel spectral radius is 0.9992292 estimated iterations to convergence 284 setup time was (sec) 1.760000 now iterating at: 13:59:48 rms-change max change #iterations 9.484068 372.9463 at 10iterations 5.444481 134.0388 at 20iterations 3.102730 77.10652 at 30iterations 1.767820 36.46315 at 40iterations 1.004736 19.71350 at 50iterations 0.5721270 10.20789 at 60iterations 0.3250220 7.953508 at 70iterations 0.1842920 3.536260 at 80iterations 0.1047888 1.882467 at 90iterations 5.9576325E-02 1.151031 at 100iterations 3.3782925E-02 0.6316566 at 110iterations 1.9143810E-02 0.3844910 at 120iterations 1.0880999E-02 0.2212257 at 130iterations 6.1862995E-03 0.1109049 at 140iterations 3.5013410E-03 7.8223228E-02 at 150iterations 1.9895826E-03 3.6978722E-02 at 160iterations 1.1281497E-03 1.9943237E-02 at 170iterations 6.4146891E-04 1.1840820E-02 at 180iterations finished qdiffx linear iterations at : 14:00:06 total time elapsed so far: 19.73000 # loops : 180 mean,max change (kT/e) : 6.4146891E-04 1.1840820E-02 energy calculations done at 19.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.89000 DelPhi exited at 14:00:07 19.897u 0.467s 0:20.79 97.8% 0+0k 0+0io 0pf+0w