Tue Oct 11 03:56:04 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 03:56:05 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 = 2714 !!! WARNING: GLU 257 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6481565 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): -11.63800 37.02700 ymin,ymax (A): -25.87200 22.30800 zmin,zma (A): -9.497000 45.42800 x,y,z range (A): 48.66500 48.18000 54.92500 scale (grids/A): 0.6481565 object centre (A): 12.69450 -1.782000 17.96550 number of atom coordinates read : 2714 total number of charged atoms : 2566 net assigned charge : 0.2280126 assigned positive charge : 408.6026 centred at (gu) : 90.33241 90.25710 91.71085 assigned negative charge : -408.3753 centred at (gu) : 90.07678 90.12045 91.64466 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7620 nv = 96 ne = 84 npr = 55729 no. pairs analyzed = 55729 no. exposed pairs = 3308 no. arc points = 23237 no. surface atoms = 1109 nbur = 1605 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 383 mr = 4299 m= 0 mr = 41 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.3800000 number of dielectric boundary points 3663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2269 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9827761E-09 1.4673548E-08 midg,1,midg; midg,igrid,midg -1.9915023E-08 2.1796897E-08 1,midg,midg; igrid,midg,midg -3.7209766E-08 4.0837822E-08 gauss-seidel spectral radius is 0.9876723 estimated iterations to convergence 74 setup time was (sec) 0.6600000 now iterating at: 03:56:05 rms-change max change #iterations 0.1595796 24.84882 at 10iterations 1.6785445E-02 2.302593 at 20iterations 1.8036868E-03 0.2398491 at 30iterations 2.3199597E-04 3.4614563E-02 at 40iterations 4.6925703E-05 5.5046082E-03 at 50iterations finished qdiffx linear iterations at : 03:56:09 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 4.6925703E-05 5.5046082E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 03:56:09 4.121u 0.242s 0:04.69 92.9% 0+0k 0+0io 6pf+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 03:56:09 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 = 2714 !!! WARNING: GLU 257 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.944470 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): -11.63800 37.02700 ymin,ymax (A): -25.87200 22.30800 zmin,zma (A): -9.497000 45.42800 x,y,z range (A): 48.66500 48.18000 54.92500 scale (grids/A): 1.944470 object centre (A): 12.69450 -1.782000 17.96550 number of atom coordinates read : 2714 total number of charged atoms : 2566 net assigned charge : 0.2280126 assigned positive charge : 408.6026 centred at (gu) : 90.99649 90.77052 95.13178 assigned negative charge : -408.3753 centred at (gu) : 90.23002 90.36093 94.93362 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 81895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23237 grid for indexing accessible points = 1.400000 m= 29915 mr = 57778 m= 4679 mr = 22133 m= 299 mr = 2938 m= 5 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2506 time to turn everything in is 0.7100000 number of dielectric boundary points 33835 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20206 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) : 0.6481565 object centre at (A) : 12.69450 -1.782000 17.96550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5905648E-02 -8.2125412E-03 midg,1,midg; midg,igrid,midg -1.2478436E-02 2.5268203E-02 1,midg,midg; igrid,midg,midg -1.5814330E-02 5.9397284E-02 gauss-seidel spectral radius is 0.9986997 estimated iterations to convergence 220 setup time was (sec) 1.010000 now iterating at: 03:56:11 rms-change max change #iterations 4.553448 192.7259 at 10iterations 2.188479 69.12484 at 20iterations 1.044614 33.04447 at 30iterations 0.4992131 15.24767 at 40iterations 0.2381947 7.585721 at 50iterations 0.1139958 3.578519 at 60iterations 5.4695792E-02 1.534852 at 70iterations 2.6104972E-02 0.7996063 at 80iterations 1.2483875E-02 0.4177680 at 90iterations 5.9894123E-03 0.1885996 at 100iterations 2.8629298E-03 8.8073730E-02 at 110iterations 1.3761861E-03 4.0519714E-02 at 120iterations finished qdiffx linear iterations at : 03:56:19 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 1.3761861E-03 4.0519714E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 03:56:20 9.595u 0.317s 0:10.40 95.1% 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 03:56:20 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 = 2714 !!! WARNING: GLU 257 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.916704 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): -11.63800 37.02700 ymin,ymax (A): -25.87200 22.30800 zmin,zma (A): -9.497000 45.42800 x,y,z range (A): 48.66500 48.18000 54.92500 scale (grids/A): 2.916704 object centre (A): 12.69450 -1.782000 17.96550 number of atom coordinates read : 2714 total number of charged atoms : 2566 net assigned charge : 0.2280126 assigned positive charge : 408.6026 centred at (gu) : 91.49473 91.15576 97.69755 assigned negative charge : -408.3753 centred at (gu) : 90.34489 90.54147 97.40034 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 189097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23237 grid for indexing accessible points = 1.400000 m= 97067 mr = 139469 m= 35242 mr = 79787 m= 8474 mr = 28462 m= 1273 mr = 6330 m= 87 mr = 863 m= 0 mr = 37 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 8524 time to turn everything in is 1.880000 number of dielectric boundary points 76292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 20526 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) : 1.944470 object centre at (A) : 12.69450 -1.782000 17.96550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7039849 0.1236454 midg,1,midg; midg,igrid,midg -0.1234369 0.3146247 1,midg,midg; igrid,midg,midg -9.5009625E-02 0.5143498 gauss-seidel spectral radius is 0.9992707 estimated iterations to convergence 292 setup time was (sec) 2.230000 now iterating at: 03:56:22 rms-change max change #iterations 10.48974 421.7703 at 10iterations 6.148942 151.4497 at 20iterations 3.586379 69.50979 at 30iterations 2.090171 49.28309 at 40iterations 1.218440 24.57493 at 50iterations 0.7066216 13.64503 at 60iterations 0.4099425 7.268586 at 70iterations 0.2376030 4.410707 at 80iterations 0.1377911 2.511459 at 90iterations 7.9901017E-02 1.590226 at 100iterations 4.6316996E-02 0.7801208 at 110iterations 2.6805338E-02 0.4995995 at 120iterations 1.5503970E-02 0.3235826 at 130iterations 9.0334769E-03 0.1545868 at 140iterations 5.2564745E-03 0.1031842 at 150iterations 3.0823608E-03 5.3024292E-02 at 160iterations 1.8246414E-03 3.3821106E-02 at 170iterations 1.1011183E-03 2.0286560E-02 at 180iterations finished qdiffx linear iterations at : 03:56:36 total time elapsed so far: 16.13000 # loops : 180 mean,max change (kT/e) : 1.1011183E-03 2.0286560E-02 energy calculations done at 16.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.30000 DelPhi exited at 03:56:37 16.302u 0.300s 0:17.17 96.6% 0+0k 0+0io 0pf+0w