Tue Oct 11 03:22:41 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 Tue Oct 11 2011 at 03:22:41 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5487983 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): -6.485000 45.45300 ymin,ymax (A): -47.87000 16.99900 zmin,zma (A): -20.14900 34.45500 x,y,z range (A): 51.93800 64.86900 54.60400 scale (grids/A): 0.5487983 object centre (A): 19.48400 -15.43550 7.153001 number of atom coordinates read : 3036 total number of charged atoms : 2896 net assigned charge : 4.528034 assigned positive charge : 454.1209 centred at (gu) : 89.44647 90.55191 89.42226 assigned negative charge : -449.5943 centred at (gu) : 89.45868 90.53549 89.40630 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6023 nv = 96 ne = 84 npr = 59807 no. pairs analyzed = 59807 no. exposed pairs = 4320 no. arc points = 30464 no. surface atoms = 1419 nbur = 1617 mkacc time = 0.1100000 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 = 1.540000 m= 262 mr = 2848 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7808 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2256155E-10 3.7636833E-10 midg,1,midg; midg,igrid,midg 1.6829363E-10 4.9876292E-10 1,midg,midg; igrid,midg,midg 4.6297088E-10 1.9568037E-10 gauss-seidel spectral radius is 0.9828959 estimated iterations to convergence 63 setup time was (sec) 0.4300000 now iterating at: 03:22:41 rms-change max change #iterations 7.5208828E-02 12.43968 at 10iterations 5.4747392E-03 0.8831162 at 20iterations 5.3253683E-04 8.8181973E-02 at 30iterations 9.1155765E-05 1.6584396E-02 at 40iterations 1.9821573E-05 3.6334991E-03 at 50iterations finished qdiffx linear iterations at : 03:22:44 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.9821573E-05 3.6334991E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 03:22:45 3.452u 0.175s 0:03.94 91.8% 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 Tue Oct 11 2011 at 03:22:45 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.646395 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): -6.485000 45.45300 ymin,ymax (A): -47.87000 16.99900 zmin,zma (A): -20.14900 34.45500 x,y,z range (A): 51.93800 64.86900 54.60400 scale (grids/A): 1.646395 object centre (A): 19.48400 -15.43550 7.153001 number of atom coordinates read : 3036 total number of charged atoms : 2896 net assigned charge : 4.528034 assigned positive charge : 454.1209 centred at (gu) : 88.33850 91.65513 88.26600 assigned negative charge : -449.5943 centred at (gu) : 88.37572 91.60619 88.21848 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 65726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30464 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20472 mr = 42117 m= 2482 mr = 13460 m= 72 mr = 1273 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 31894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 303 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 22292 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) : 0.5487983 object centre at (A) : 19.48400 -15.43550 7.153001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4654276E-03 3.4971505E-03 midg,1,midg; midg,igrid,midg 5.1428811E-03 5.5692457E-03 1,midg,midg; igrid,midg,midg 3.9409432E-03 7.8884726E-03 gauss-seidel spectral radius is 0.9982466 estimated iterations to convergence 190 setup time was (sec) 0.5600000 now iterating at: 03:22:45 rms-change max change #iterations 3.415290 134.4053 at 10iterations 1.433794 54.71889 at 20iterations 0.6048353 24.54063 at 30iterations 0.2555777 9.129570 at 40iterations 0.1077737 4.463640 at 50iterations 4.5485135E-02 1.579147 at 60iterations 1.9352816E-02 0.6945477 at 70iterations 8.1805205E-03 0.2888412 at 80iterations 3.4736795E-03 0.1210403 at 90iterations 1.4720812E-03 6.0187817E-02 at 100iterations 6.3155906E-04 2.4848938E-02 at 110iterations 2.7021911E-04 9.5915794E-03 at 120iterations finished qdiffx linear iterations at : 03:22:52 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.7021911E-04 9.5915794E-03 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 03:22:53 7.790u 0.196s 0:08.28 96.3% 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 03:22:53 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! WARNING: HIR 350 has a net charge of 0.5140 !!! WARNING: HIR 476 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.469592 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): -6.485000 45.45300 ymin,ymax (A): -47.87000 16.99900 zmin,zma (A): -20.14900 34.45500 x,y,z range (A): 51.93800 64.86900 54.60400 scale (grids/A): 2.469592 object centre (A): 19.48400 -15.43550 7.153001 number of atom coordinates read : 3036 total number of charged atoms : 2896 net assigned charge : 4.528034 assigned positive charge : 454.1209 centred at (gu) : 87.50748 92.48256 87.39886 assigned negative charge : -449.5943 centred at (gu) : 87.56346 92.40910 87.32763 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30464 grid for indexing accessible points = 1.400000 m= 69142 mr = 103933 m= 21304 mr = 52929 m= 3957 mr = 15590 m= 334 mr = 2663 m= 4 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 72034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 23143 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) : 1.646395 object centre at (A) : 19.48400 -15.43550 7.153001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1781637 2.2118757E-02 midg,1,midg; midg,igrid,midg 8.9268841E-02 4.6139739E-02 1,midg,midg; igrid,midg,midg 9.0595350E-02 0.1851466 gauss-seidel spectral radius is 0.9991694 estimated iterations to convergence 274 setup time was (sec) 1.050000 now iterating at: 03:22:54 rms-change max change #iterations 8.933736 259.1075 at 10iterations 5.136509 135.9991 at 20iterations 2.911058 66.62728 at 30iterations 1.650887 39.13383 at 40iterations 0.9288679 19.64964 at 50iterations 0.5228276 12.00152 at 60iterations 0.2934862 5.940263 at 70iterations 0.1643350 3.614883 at 80iterations 9.1679916E-02 1.838419 at 90iterations 5.1208276E-02 1.113205 at 100iterations 2.8498206E-02 0.5628963 at 110iterations 1.5901104E-02 0.3449278 at 120iterations 8.8626156E-03 0.1981316 at 130iterations 4.9341694E-03 9.8337173E-02 at 140iterations 2.7486326E-03 5.6886673E-02 at 150iterations 1.5336373E-03 3.1221390E-02 at 160iterations 8.5355586E-04 1.8451691E-02 at 170iterations 4.7630837E-04 1.0015965E-02 at 180iterations finished qdiffx linear iterations at : 03:23:06 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 4.7630837E-04 1.0015965E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 03:23:06 12.572u 0.193s 0:13.18 96.8% 0+0k 0+0io 0pf+0w