Tue Oct 11 07:54:03 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 07:54:03 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 = 2402 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: 0.6434820 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): -1.501000 53.82300 ymin,ymax (A): -22.66400 22.82900 zmin,zma (A): 9.075999 54.61100 x,y,z range (A): 55.32400 45.49300 45.53500 scale (grids/A): 0.6434820 object centre (A): 26.16100 8.2499504E-02 31.84350 number of atom coordinates read : 2402 total number of charged atoms : 2266 net assigned charge : 6.500008 assigned positive charge : 362.4742 centred at (gu) : 88.53575 90.15380 89.85043 assigned negative charge : -355.9747 centred at (gu) : 88.57522 90.11627 89.68887 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6699 nv = 96 ne = 84 npr = 48397 no. pairs analyzed = 48397 no. exposed pairs = 2891 no. arc points = 20246 no. surface atoms = 980 nbur = 1422 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 383 mr = 3785 m= 0 mr = 35 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1998 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2144345E-09 2.8121919E-08 midg,1,midg; midg,igrid,midg 5.7977525E-09 1.5267602E-08 1,midg,midg; igrid,midg,midg 2.0441151E-08 4.3236317E-09 gauss-seidel spectral radius is 0.9874676 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 07:54:03 rms-change max change #iterations 0.1430404 22.55203 at 10iterations 1.4760552E-02 1.925081 at 20iterations 1.5840154E-03 0.2454853 at 30iterations 2.0388524E-04 3.0279160E-02 at 40iterations 3.5085006E-05 5.7601929E-03 at 50iterations finished qdiffx linear iterations at : 07:54:06 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 3.5085006E-05 5.7601929E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 07:54:06 3.119u 0.128s 0:03.55 90.9% 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 Tue Oct 11 2011 at 07:54:06 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 = 2402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.930446 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): -1.501000 53.82300 ymin,ymax (A): -22.66400 22.82900 zmin,zma (A): 9.075999 54.61100 x,y,z range (A): 55.32400 45.49300 45.53500 scale (grids/A): 1.930446 object centre (A): 26.16100 8.2499504E-02 31.84350 number of atom coordinates read : 2402 total number of charged atoms : 2266 net assigned charge : 6.500008 assigned positive charge : 362.4742 centred at (gu) : 85.60662 90.46090 89.55099 assigned negative charge : -355.9747 centred at (gu) : 85.72570 90.34859 89.06656 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20246 grid for indexing accessible points = 1.400000 m= 26989 mr = 50551 m= 4055 mr = 20203 m= 235 mr = 2453 m= 0 mr = 88 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.5500000 number of dielectric boundary points 30049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17842 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) : 0.6434820 object centre at (A) : 26.16100 8.2499504E-02 31.84350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7592803E-02 4.1419048E-02 midg,1,midg; midg,igrid,midg 8.1404182E-04 7.8308936E-03 1,midg,midg; igrid,midg,midg 2.2632575E-02 2.5313228E-02 gauss-seidel spectral radius is 0.9986500 estimated iterations to convergence 216 setup time was (sec) 0.8400000 now iterating at: 07:54:07 rms-change max change #iterations 4.164618 188.9424 at 10iterations 1.954437 69.73453 at 20iterations 0.9265708 29.50795 at 30iterations 0.4358234 14.49184 at 40iterations 0.2061305 7.155025 at 50iterations 9.6912906E-02 3.381577 at 60iterations 4.5749124E-02 1.416037 at 70iterations 2.1501906E-02 0.7475605 at 80iterations 1.0207411E-02 0.3306770 at 90iterations 4.8241657E-03 0.1575518 at 100iterations 2.2978259E-03 8.1771851E-02 at 110iterations 1.0968358E-03 3.7712097E-02 at 120iterations finished qdiffx linear iterations at : 07:54:13 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 1.0968358E-03 3.7712097E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 07:54:14 6.921u 0.172s 0:07.85 90.3% 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 Tue Oct 11 2011 at 07:54:14 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 = 2402 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: 2.895669 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): -1.501000 53.82300 ymin,ymax (A): -22.66400 22.82900 zmin,zma (A): 9.075999 54.61100 x,y,z range (A): 55.32400 45.49300 45.53500 scale (grids/A): 2.895669 object centre (A): 26.16100 8.2499504E-02 31.84350 number of atom coordinates read : 2402 total number of charged atoms : 2266 net assigned charge : 6.500008 assigned positive charge : 362.4742 centred at (gu) : 83.40982 90.69135 89.32631 assigned negative charge : -355.9747 centred at (gu) : 83.58861 90.52271 88.59974 start vw surface at 0.2000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 166397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20246 grid for indexing accessible points = 1.400000 m= 87307 mr = 121979 m= 31782 mr = 72271 m= 7114 mr = 25632 m= 977 mr = 5147 m= 56 mr = 661 m= 0 mr = 36 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 1032 time to turn everything in is 1.320000 number of dielectric boundary points 67907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 18122 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) : 1.930446 object centre at (A) : 26.16100 8.2499504E-02 31.84350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2593181 0.4200156 midg,1,midg; midg,igrid,midg -1.7835800E-02 -3.9766938E-03 1,midg,midg; igrid,midg,midg 7.4386761E-02 0.1818485 gauss-seidel spectral radius is 0.9992541 estimated iterations to convergence 289 setup time was (sec) 1.590000 now iterating at: 07:54:16 rms-change max change #iterations 9.677916 405.6802 at 10iterations 5.650449 134.5175 at 20iterations 3.286716 77.67740 at 30iterations 1.900508 47.06997 at 40iterations 1.100508 25.38054 at 50iterations 0.6339185 13.48495 at 60iterations 0.3659837 6.678574 at 70iterations 0.2101645 4.285220 at 80iterations 0.1212105 2.263481 at 90iterations 6.9569625E-02 1.411396 at 100iterations 3.9906852E-02 0.7051735 at 110iterations 2.2956133E-02 0.4207249 at 120iterations 1.3175013E-02 0.2506026 at 130iterations 7.5785727E-03 0.1370392 at 140iterations 4.3619419E-03 7.8876495E-02 at 150iterations 2.5104210E-03 4.9818039E-02 at 160iterations 1.4551762E-03 2.9802799E-02 at 170iterations 8.4986666E-04 1.6181946E-02 at 180iterations finished qdiffx linear iterations at : 07:54:26 total time elapsed so far: 11.22000 # loops : 180 mean,max change (kT/e) : 8.4986666E-04 1.6181946E-02 energy calculations done at 11.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 07:54:27 11.391u 0.178s 0:12.16 95.0% 0+0k 0+0io 0pf+0w