Sun Oct 9 08:53:02 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 08:53:02 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5608 !!! WARNING: HIR 701 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5164810 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): 8.207999 77.13600 ymin,ymax (A): 2.303000 66.08100 zmin,zma (A): -18.40800 50.20800 x,y,z range (A): 68.92800 63.77800 68.61600 scale (grids/A): 0.5164810 object centre (A): 42.67200 34.19200 15.90000 number of atom coordinates read : 5608 total number of charged atoms : 5442 net assigned charge : -3.485982 assigned positive charge : 845.9520 centred at (gu) : 89.64652 89.52179 89.21844 assigned negative charge : -849.4448 centred at (gu) : 89.53938 89.61382 89.23579 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9344 nv = 96 ne = 84 npr = 114982 no. pairs analyzed = 114982 no. exposed pairs = 6845 no. arc points = 47709 no. surface atoms = 2311 nbur = 3297 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 297 mr = 4880 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4683 ## 709 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 12569 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4426212E-12 -1.0908476E-10 midg,1,midg; midg,igrid,midg 3.3529243E-10 -3.8203704E-10 1,midg,midg; igrid,midg,midg -5.4288740E-10 3.2142344E-10 gauss-seidel spectral radius is 0.9808816 estimated iterations to convergence 60 setup time was (sec) 0.5600000 now iterating at: 08:53:02 rms-change max change #iterations 7.8517251E-02 12.09301 at 10iterations 4.6967245E-03 0.7440224 at 20iterations 4.2060978E-04 8.5790634E-02 at 30iterations 9.4516632E-05 2.2806168E-02 at 40iterations 2.8174092E-05 6.5345764E-03 at 50iterations finished qdiffx linear iterations at : 08:53:05 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 2.8174092E-05 6.5345764E-03 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 08:53:06 3.645u 0.175s 0:04.10 92.9% 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 08:53:06 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5608 !!! WARNING: HIR 701 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.549443 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): 8.207999 77.13600 ymin,ymax (A): 2.303000 66.08100 zmin,zma (A): -18.40800 50.20800 x,y,z range (A): 68.92800 63.77800 68.61600 scale (grids/A): 1.549443 object centre (A): 42.67200 34.19200 15.90000 number of atom coordinates read : 5608 total number of charged atoms : 5442 net assigned charge : -3.485982 assigned positive charge : 845.9520 centred at (gu) : 88.93771 88.56318 87.65378 assigned negative charge : -849.4448 centred at (gu) : 88.61798 88.84148 87.70731 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 105774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47709 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 29258 mr = 73003 m= 2402 mr = 18857 m= 48 mr = 956 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 959 time to turn everything in is 0.5100000 number of dielectric boundary points 44666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 655 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 41116 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) : 0.5164810 object centre at (A) : 42.67200 34.19200 15.90000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4568252E-02 -2.1219425E-02 midg,1,midg; midg,igrid,midg 9.8875258E-03 -4.3658265E-03 1,midg,midg; igrid,midg,midg -2.0858267E-02 5.8818380E-03 gauss-seidel spectral radius is 0.9982330 estimated iterations to convergence 189 setup time was (sec) 0.7500000 now iterating at: 08:53:07 rms-change max change #iterations 4.261686 173.0680 at 10iterations 1.793418 52.89087 at 20iterations 0.7571978 24.23129 at 30iterations 0.3210306 9.673464 at 40iterations 0.1352813 4.079765 at 50iterations 5.7102278E-02 1.733456 at 60iterations 2.4168130E-02 0.7475891 at 70iterations 1.0213095E-02 0.3047266 at 80iterations 4.3437118E-03 0.1212234 at 90iterations 1.8543139E-03 5.7208061E-02 at 100iterations 7.9831568E-04 2.2300720E-02 at 110iterations 3.5175445E-04 1.1962891E-02 at 120iterations finished qdiffx linear iterations at : 08:53:14 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 3.5175445E-04 1.1962891E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 08:53:15 8.181u 0.207s 0:08.73 95.9% 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 08:53:15 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5608 !!! WARNING: HIR 701 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.324164 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): 8.207999 77.13600 ymin,ymax (A): 2.303000 66.08100 zmin,zma (A): -18.40800 50.20800 x,y,z range (A): 68.92800 63.77800 68.61600 scale (grids/A): 2.324164 object centre (A): 42.67200 34.19200 15.90000 number of atom coordinates read : 5608 total number of charged atoms : 5442 net assigned charge : -3.485982 assigned positive charge : 845.9520 centred at (gu) : 88.40630 87.84447 86.48016 assigned negative charge : -849.4448 centred at (gu) : 87.92686 88.26200 86.56096 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 247054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47709 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 106594 mr = 180008 m= 25601 mr = 82192 m= 3335 mr = 17884 m= 152 mr = 1908 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 3470 time to turn everything in is 1.250000 number of dielectric boundary points 100705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 43430 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) : 1.549443 object centre at (A) : 42.67200 34.19200 15.90000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3488462 -0.5408196 midg,1,midg; midg,igrid,midg 0.1889197 -5.9723780E-02 1,midg,midg; igrid,midg,midg -0.6441352 7.6540865E-02 gauss-seidel spectral radius is 0.9992204 estimated iterations to convergence 283 setup time was (sec) 1.500000 now iterating at: 08:53:16 rms-change max change #iterations 11.51989 322.0092 at 10iterations 6.769407 133.4695 at 20iterations 3.950695 80.70331 at 30iterations 2.290947 53.36081 at 40iterations 1.324926 29.50134 at 50iterations 0.7624533 15.47657 at 60iterations 0.4380329 8.193281 at 70iterations 0.2516654 4.943166 at 80iterations 0.1437947 2.368043 at 90iterations 8.2236290E-02 1.712809 at 100iterations 4.6997972E-02 0.8056183 at 110iterations 2.6793873E-02 0.4847870 at 120iterations 1.5260036E-02 0.2872820 at 130iterations 8.6917495E-03 0.1385269 at 140iterations 4.9579516E-03 8.6372375E-02 at 150iterations 2.8312567E-03 5.1786423E-02 at 160iterations 1.6156554E-03 2.8694153E-02 at 170iterations 9.2285406E-04 1.5618086E-02 at 180iterations finished qdiffx linear iterations at : 08:53:28 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 9.2285406E-04 1.5618086E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.79000 DelPhi exited at 08:53:29 13.789u 0.223s 0:14.29 97.9% 0+0k 0+0io 0pf+0w