Tue Oct 11 08:33:39 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 08:33:39 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2130 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7163410 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): -19.85000 26.48400 ymin,ymax (A): -12.10300 28.45900 zmin,zma (A): -2.698000 46.99900 x,y,z range (A): 46.33400 40.56200 49.69700 scale (grids/A): 0.7163410 object centre (A): 3.317000 8.177999 22.15050 number of atom coordinates read : 2130 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.7059 centred at (gu) : 89.39970 89.64648 90.66015 assigned negative charge : -321.6671 centred at (gu) : 89.25790 89.66319 90.73978 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7411 nv = 96 ne = 84 npr = 42949 no. pairs analyzed = 42949 no. exposed pairs = 2544 no. arc points = 17117 no. surface atoms = 869 nbur = 1261 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4369 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1614 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9371384E-08 1.5338919E-08 midg,1,midg; midg,igrid,midg 7.9124334E-08 4.9973199E-08 1,midg,midg; igrid,midg,midg -2.9168353E-08 1.3400876E-07 gauss-seidel spectral radius is 0.9898412 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 08:33:40 rms-change max change #iterations 0.2188854 30.61998 at 10iterations 2.7955726E-02 3.985992 at 20iterations 3.6918411E-03 0.4562035 at 30iterations 5.3626439E-04 6.9419861E-02 at 40iterations 1.0298286E-04 1.4427185E-02 at 50iterations finished qdiffx linear iterations at : 08:33:43 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.0298286E-04 1.4427185E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:33:43 3.345u 0.162s 0:04.27 81.9% 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 08:33:43 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2130 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.149023 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): -19.85000 26.48400 ymin,ymax (A): -12.10300 28.45900 zmin,zma (A): -2.698000 46.99900 x,y,z range (A): 46.33400 40.56200 49.69700 scale (grids/A): 2.149023 object centre (A): 3.317000 8.177999 22.15050 number of atom coordinates read : 2130 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.7059 centred at (gu) : 88.19921 88.93947 91.98020 assigned negative charge : -321.6671 centred at (gu) : 87.77384 88.98956 92.21915 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 77912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17117 grid for indexing accessible points = 1.400000 m= 31705 mr = 55804 m= 6430 mr = 24318 m= 592 mr = 4332 m= 19 mr = 284 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15888 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) : 0.7163410 object centre at (A) : 3.317000 8.177999 22.15050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8948264E-02 6.5191895E-02 midg,1,midg; midg,igrid,midg 3.0348655E-02 4.1198577E-03 1,midg,midg; igrid,midg,midg 4.5801122E-03 3.7207741E-02 gauss-seidel spectral radius is 0.9988574 estimated iterations to convergence 234 setup time was (sec) 0.6100000 now iterating at: 08:33:44 rms-change max change #iterations 4.816954 170.8243 at 10iterations 2.405328 77.90192 at 20iterations 1.211415 35.80179 at 30iterations 0.6003603 17.03941 at 40iterations 0.3029765 8.932438 at 50iterations 0.1513992 4.310431 at 60iterations 7.6127984E-02 2.263839 at 70iterations 3.8110435E-02 1.134329 at 80iterations 1.9144619E-02 0.5545473 at 90iterations 9.6372459E-03 0.2741442 at 100iterations 4.8520258E-03 0.1625214 at 110iterations 2.4766915E-03 7.2551727E-02 at 120iterations finished qdiffx linear iterations at : 08:33:51 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.4766915E-03 7.2551727E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 08:33:52 7.756u 0.200s 0:08.64 92.0% 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 08:33:52 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2130 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.223535 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): -19.85000 26.48400 ymin,ymax (A): -12.10300 28.45900 zmin,zma (A): -2.698000 46.99900 x,y,z range (A): 46.33400 40.56200 49.69700 scale (grids/A): 3.223535 object centre (A): 3.317000 8.177999 22.15050 number of atom coordinates read : 2130 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.7059 centred at (gu) : 87.29882 88.40920 92.97028 assigned negative charge : -321.6671 centred at (gu) : 86.66079 88.48425 93.32866 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 179584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17117 grid for indexing accessible points = 1.400000 m= 98383 mr = 133990 m= 40814 mr = 82313 m= 12096 mr = 33912 m= 2377 mr = 9397 m= 254 mr = 1672 m= 3 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.6100001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.210000 number of dielectric boundary points 72093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 15996 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) : 2.149023 object centre at (A) : 3.317000 8.177999 22.15050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3624761 0.7877204 midg,1,midg; midg,igrid,midg 0.2268219 -1.8421218E-02 1,midg,midg; igrid,midg,midg 0.2130013 0.3283236 gauss-seidel spectral radius is 0.9993017 estimated iterations to convergence 299 setup time was (sec) 1.450000 now iterating at: 08:33:54 rms-change max change #iterations 10.63991 463.6859 at 10iterations 6.316923 128.9887 at 20iterations 3.733163 66.24180 at 30iterations 2.204830 40.53490 at 40iterations 1.299480 22.50653 at 50iterations 0.7630851 12.78130 at 60iterations 0.4495839 7.317894 at 70iterations 0.2639282 4.392936 at 80iterations 0.1548633 2.929430 at 90iterations 9.0985440E-02 1.557827 at 100iterations 5.3573936E-02 0.8884258 at 110iterations 3.1682294E-02 0.5243073 at 120iterations 1.8776374E-02 0.3185124 at 130iterations 1.1299104E-02 0.2089310 at 140iterations 6.9286278E-03 0.1273804 at 150iterations 4.3602260E-03 7.9208374E-02 at 160iterations 2.8712263E-03 5.2520752E-02 at 170iterations 1.9958306E-03 4.1877747E-02 at 180iterations finished qdiffx linear iterations at : 08:34:05 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.9958306E-03 4.1877747E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 08:34:06 12.815u 0.192s 0:13.60 95.5% 0+0k 0+0io 0pf+0w