Sun Oct 9 06:22:35 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 06:22:35 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1988 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -0.2720 !!! WARNING: NDP 202 has a net charge of -3.0000 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: 0.7369837 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): -3.291000 39.19300 ymin,ymax (A): 5.689000 46.83300 zmin,zma (A): 8.419000 56.72400 x,y,z range (A): 42.48400 41.14400 48.30500 scale (grids/A): 0.7369837 object centre (A): 17.95100 26.26100 32.57150 number of atom coordinates read : 1988 total number of charged atoms : 1845 net assigned charge : -1.246986 assigned positive charge : 298.2260 centred at (gu) : 90.67786 89.69812 90.30382 assigned negative charge : -299.4731 centred at (gu) : 90.73067 89.79755 90.13541 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7419 nv = 96 ne = 84 npr = 41932 no. pairs analyzed = 41932 no. exposed pairs = 2391 no. arc points = 17013 no. surface atoms = 802 nbur = 1186 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 511 mr = 4269 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 58 time to turn everything in is 0.2500000 number of dielectric boundary points 3553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1482 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7880 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6398364E-07 1.3500403E-07 midg,1,midg; midg,igrid,midg 7.1284546E-08 -1.0436867E-07 1,midg,midg; igrid,midg,midg 2.2791808E-08 -7.7642319E-08 gauss-seidel spectral radius is 0.9903916 estimated iterations to convergence 83 setup time was (sec) 0.5100000 now iterating at: 06:22:35 rms-change max change #iterations 0.2355343 36.24371 at 10iterations 3.2129977E-02 4.518959 at 20iterations 4.2574592E-03 0.5152245 at 30iterations 5.7021447E-04 7.4040413E-02 at 40iterations 7.5878888E-05 1.0161400E-02 at 50iterations finished qdiffx linear iterations at : 06:22:38 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.5878888E-05 1.0161400E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 06:22:39 3.435u 0.227s 0:03.93 92.8% 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 06:22:39 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1988 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -0.2720 !!! WARNING: NDP 202 has a net charge of -3.0000 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: 2.210951 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): -3.291000 39.19300 ymin,ymax (A): 5.689000 46.83300 zmin,zma (A): 8.419000 56.72400 x,y,z range (A): 42.48400 41.14400 48.30500 scale (grids/A): 2.210951 object centre (A): 17.95100 26.26100 32.57150 number of atom coordinates read : 1988 total number of charged atoms : 1845 net assigned charge : -1.246986 assigned positive charge : 298.2260 centred at (gu) : 92.03353 89.09413 90.91144 assigned negative charge : -299.4731 centred at (gu) : 92.19193 89.39284 90.40618 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78537 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17013 grid for indexing accessible points = 1.400000 m= 31168 mr = 55368 m= 6640 mr = 23950 m= 690 mr = 4747 m= 42 mr = 346 m= 0 mr = 13 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1982 time to turn everything in is 0.5700000 number of dielectric boundary points 32653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14710 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) : 0.7369837 object centre at (A) : 17.95100 26.26100 32.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2571967E-02 6.5936251E-03 midg,1,midg; midg,igrid,midg 2.4706563E-02 4.7034789E-03 1,midg,midg; igrid,midg,midg -8.1980741E-03 -1.4150029E-02 gauss-seidel spectral radius is 0.9989067 estimated iterations to convergence 239 setup time was (sec) 0.8900000 now iterating at: 06:22:40 rms-change max change #iterations 4.945835 194.9233 at 10iterations 2.506063 81.28929 at 20iterations 1.267897 41.76842 at 30iterations 0.6478652 19.86443 at 40iterations 0.3274443 9.841960 at 50iterations 0.1658835 4.939941 at 60iterations 8.4359214E-02 2.692947 at 70iterations 4.2872414E-02 1.203575 at 80iterations 2.1668443E-02 0.6630054 at 90iterations 1.1011828E-02 0.3334808 at 100iterations 5.5886065E-03 0.1606674 at 110iterations 2.8263514E-03 7.5983047E-02 at 120iterations finished qdiffx linear iterations at : 06:22:47 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 2.8263514E-03 7.5983047E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 06:22:47 7.904u 0.270s 0:08.43 96.9% 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 Sun Oct 9 2011 at 06:22:47 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1988 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -0.2720 !!! WARNING: NDP 202 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.316427 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): -3.291000 39.19300 ymin,ymax (A): 5.689000 46.83300 zmin,zma (A): 8.419000 56.72400 x,y,z range (A): 42.48400 41.14400 48.30500 scale (grids/A): 3.316427 object centre (A): 17.95100 26.26100 32.57150 number of atom coordinates read : 1988 total number of charged atoms : 1845 net assigned charge : -1.246986 assigned positive charge : 298.2260 centred at (gu) : 93.05032 88.64143 91.36729 assigned negative charge : -299.4731 centred at (gu) : 93.28788 89.08923 90.60925 start vw surface at 0.1100000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 180672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17013 grid for indexing accessible points = 1.400000 m= 96709 mr = 132719 m= 40232 mr = 81102 m= 12894 mr = 33630 m= 2815 mr = 10357 m= 419 mr = 2069 m= 40 mr = 271 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 7097 time to turn everything in is 1.810000 number of dielectric boundary points 73606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 14756 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) : 2.210951 object centre at (A) : 17.95100 26.26100 32.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3119957 0.1212360 midg,1,midg; midg,igrid,midg 0.3314097 3.0362042E-02 1,midg,midg; igrid,midg,midg -0.1087705 -8.0262922E-02 gauss-seidel spectral radius is 0.9993057 estimated iterations to convergence 299 setup time was (sec) 2.140000 now iterating at: 06:22:50 rms-change max change #iterations 10.58858 307.4465 at 10iterations 6.163394 119.7603 at 20iterations 3.599786 64.07089 at 30iterations 2.098992 36.45893 at 40iterations 1.226273 20.83692 at 50iterations 0.7161087 12.61789 at 60iterations 0.4175794 6.941282 at 70iterations 0.2440312 4.023705 at 80iterations 0.1421402 2.343278 at 90iterations 8.3044410E-02 1.560050 at 100iterations 4.8401050E-02 0.7672234 at 110iterations 2.8334329E-02 0.4425011 at 120iterations 1.6540008E-02 0.2768173 at 130iterations 9.6559012E-03 0.1543732 at 140iterations 5.6230300E-03 0.1060181 at 150iterations 3.2953448E-03 5.5278778E-02 at 160iterations 1.9244024E-03 3.5367012E-02 at 170iterations 1.1244293E-03 1.9182205E-02 at 180iterations finished qdiffx linear iterations at : 06:23:01 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 1.1244293E-03 1.9182205E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 06:23:01 13.401u 0.280s 0:14.00 97.7% 0+0k 0+0io 0pf+0w