Mon Oct 10 17:02:46 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 17:02:47 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2846 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6168347 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): -8.905000 48.80900 ymin,ymax (A): -7.930000 38.89900 zmin,zma (A): 0.7129999 55.79700 x,y,z range (A): 57.71400 46.82900 55.08400 scale (grids/A): 0.6168347 object centre (A): 19.95200 15.48450 28.25500 number of atom coordinates read : 2846 total number of charged atoms : 2705 net assigned charge : -2.985972 assigned positive charge : 431.0731 centred at (gu) : 89.24265 89.62817 88.75330 assigned negative charge : -434.0602 centred at (gu) : 89.16689 89.54755 88.71429 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7426 nv = 96 ne = 84 npr = 56347 no. pairs analyzed = 56347 no. exposed pairs = 3763 no. arc points = 26670 no. surface atoms = 1276 nbur = 1570 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3924 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3100000 number of dielectric boundary points 3830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2683 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8952 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2230083E-09 3.9808476E-10 midg,1,midg; midg,igrid,midg -8.2250917E-09 3.0580891E-09 1,midg,midg; igrid,midg,midg -8.5687102E-09 2.5239237E-09 gauss-seidel spectral radius is 0.9864206 estimated iterations to convergence 70 setup time was (sec) 0.5300000 now iterating at: 17:02:47 rms-change max change #iterations 0.1335052 20.79550 at 10iterations 1.2025538E-02 1.871494 at 20iterations 1.1199005E-03 0.1617203 at 30iterations 1.0298970E-04 1.6565323E-02 at 40iterations 1.0122968E-05 1.4505386E-03 at 50iterations finished qdiffx linear iterations at : 17:02:50 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.0122968E-05 1.4505386E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 17:02:51 3.095u 0.140s 0:04.58 70.5% 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 17:02:51 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2846 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.850504 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): -8.905000 48.80900 ymin,ymax (A): -7.930000 38.89900 zmin,zma (A): 0.7129999 55.79700 x,y,z range (A): 57.71400 46.82900 55.08400 scale (grids/A): 1.850504 object centre (A): 19.95200 15.48450 28.25500 number of atom coordinates read : 2846 total number of charged atoms : 2705 net assigned charge : -2.985972 assigned positive charge : 431.0731 centred at (gu) : 87.72697 88.88367 86.25879 assigned negative charge : -434.0602 centred at (gu) : 87.50011 88.64248 86.14253 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26670 grid for indexing accessible points = 1.400000 m= 27450 mr = 54208 m= 3794 mr = 19551 m= 180 mr = 2220 m= 0 mr = 41 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1320 time to turn everything in is 0.5500000 number of dielectric boundary points 35294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21203 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) : 0.6168347 object centre at (A) : 19.95200 15.48450 28.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4554725E-04 3.1501073E-03 midg,1,midg; midg,igrid,midg -1.9487435E-02 -6.9141324E-04 1,midg,midg; igrid,midg,midg -4.7824040E-02 2.2566445E-02 gauss-seidel spectral radius is 0.9985874 estimated iterations to convergence 211 setup time was (sec) 0.8200000 now iterating at: 17:02:52 rms-change max change #iterations 4.298092 195.4117 at 10iterations 1.983245 92.43799 at 20iterations 0.9159701 29.37981 at 30iterations 0.4217832 13.18583 at 40iterations 0.1950064 5.917755 at 50iterations 9.0153188E-02 2.956820 at 60iterations 4.1611034E-02 1.300014 at 70iterations 1.9216279E-02 0.6901889 at 80iterations 8.8928407E-03 0.2760983 at 90iterations 4.1110064E-03 0.1350899 at 100iterations 1.9001743E-03 6.0997009E-02 at 110iterations 8.7766594E-04 2.7286530E-02 at 120iterations finished qdiffx linear iterations at : 17:02:58 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 8.7766594E-04 2.7286530E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 17:02:59 6.937u 0.175s 0:07.82 90.7% 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 17:02:59 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2846 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.775756 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): -8.905000 48.80900 ymin,ymax (A): -7.930000 38.89900 zmin,zma (A): 0.7129999 55.79700 x,y,z range (A): 57.71400 46.82900 55.08400 scale (grids/A): 2.775756 object centre (A): 19.95200 15.48450 28.25500 number of atom coordinates read : 2846 total number of charged atoms : 2705 net assigned charge : -2.985972 assigned positive charge : 431.0731 centred at (gu) : 86.59013 88.32540 84.38805 assigned negative charge : -434.0602 centred at (gu) : 86.25024 87.96360 84.21372 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 184989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26670 grid for indexing accessible points = 1.400000 m= 90150 mr = 132049 m= 30511 mr = 72454 m= 6515 mr = 23747 m= 764 mr = 4701 m= 31 mr = 424 m= 0 mr = 12 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 4343 time to turn everything in is 1.350000 number of dielectric boundary points 79573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 21638 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) : 1.850504 object centre at (A) : 19.95200 15.48450 28.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6186332E-02 -0.1794651 midg,1,midg; midg,igrid,midg -0.1735099 -2.2895148E-02 1,midg,midg; igrid,midg,midg -0.6380324 0.3445063 gauss-seidel spectral radius is 0.9992658 estimated iterations to convergence 291 setup time was (sec) 1.630000 now iterating at: 17:03:01 rms-change max change #iterations 10.41265 334.0534 at 10iterations 6.168922 183.5879 at 20iterations 3.621044 93.51138 at 30iterations 2.113487 47.89267 at 40iterations 1.230157 25.49183 at 50iterations 0.7149937 14.17782 at 60iterations 0.4153113 8.501301 at 70iterations 0.2401736 5.254360 at 80iterations 0.1390028 2.776672 at 90iterations 8.0378927E-02 1.524422 at 100iterations 4.6435185E-02 0.8335896 at 110iterations 2.6784824E-02 0.5232773 at 120iterations 1.5423879E-02 0.2906275 at 130iterations 8.9080110E-03 0.1702638 at 140iterations 5.1433821E-03 9.1171265E-02 at 150iterations 2.9593292E-03 5.1071167E-02 at 160iterations 1.7071345E-03 3.1309128E-02 at 170iterations 9.8480168E-04 1.9434214E-02 at 180iterations finished qdiffx linear iterations at : 17:03:11 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 9.8480168E-04 1.9434214E-02 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 17:03:12 11.739u 0.228s 0:12.54 95.2% 0+0k 0+0io 0pf+0w