Tue Oct 11 06:12:13 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 06:12:13 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: SEP 190 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.7223732 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): 0.8059999 46.23500 ymin,ymax (A): 0.6860000 40.29500 zmin,zma (A): -2.093000 47.18900 x,y,z range (A): 45.42900 39.60900 49.28200 scale (grids/A): 0.7223732 object centre (A): 23.52050 20.49050 22.54800 number of atom coordinates read : 2061 total number of charged atoms : 1931 net assigned charge : 7.025009 assigned positive charge : 314.5471 centred at (gu) : 91.25148 90.57947 90.26711 assigned negative charge : -307.5222 centred at (gu) : 91.44011 90.55265 90.30029 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7306 nv = 96 ne = 84 npr = 41357 no. pairs analyzed = 41357 no. exposed pairs = 2505 no. arc points = 16968 no. surface atoms = 852 nbur = 1209 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 512 mr = 4254 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1588 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7975 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0255856E-07 6.6178991E-08 midg,1,midg; midg,igrid,midg 6.0682360E-08 1.1539048E-07 1,midg,midg; igrid,midg,midg 1.6585376E-07 -5.8023158E-08 gauss-seidel spectral radius is 0.9900047 estimated iterations to convergence 81 setup time was (sec) 0.5200000 now iterating at: 06:12:14 rms-change max change #iterations 0.2229888 33.72557 at 10iterations 2.9542815E-02 3.989380 at 20iterations 4.0925429E-03 0.5137863 at 30iterations 7.4818166E-04 9.5809937E-02 at 40iterations 2.0635141E-04 2.6750565E-02 at 50iterations finished qdiffx linear iterations at : 06:12:17 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 2.0635141E-04 2.6750565E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:12:18 3.336u 0.202s 0:04.37 80.7% 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 06:12:18 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: SEP 190 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.167120 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): 0.8059999 46.23500 ymin,ymax (A): 0.6860000 40.29500 zmin,zma (A): -2.093000 47.18900 x,y,z range (A): 45.42900 39.60900 49.28200 scale (grids/A): 2.167120 object centre (A): 23.52050 20.49050 22.54800 number of atom coordinates read : 2061 total number of charged atoms : 1931 net assigned charge : 7.025009 assigned positive charge : 314.5471 centred at (gu) : 93.75476 91.73853 90.80157 assigned negative charge : -307.5222 centred at (gu) : 94.32040 91.65789 90.90098 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 77828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16968 grid for indexing accessible points = 1.400000 m= 32012 mr = 55669 m= 6505 mr = 24570 m= 605 mr = 4401 m= 22 mr = 318 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 32014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15358 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) : 0.7223732 object centre at (A) : 23.52050 20.49050 22.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5722969E-02 6.9840193E-02 midg,1,midg; midg,igrid,midg 4.6021529E-03 3.7791979E-02 1,midg,midg; igrid,midg,midg 4.1509096E-02 -9.7563403E-04 gauss-seidel spectral radius is 0.9988704 estimated iterations to convergence 235 setup time was (sec) 0.8600000 now iterating at: 06:12:19 rms-change max change #iterations 4.768686 190.1191 at 10iterations 2.382795 90.29617 at 20iterations 1.202096 36.03270 at 30iterations 0.6043281 18.65711 at 40iterations 0.3037966 9.059868 at 50iterations 0.1533293 4.768684 at 60iterations 7.6970562E-02 2.656929 at 70iterations 3.8985141E-02 1.115078 at 80iterations 1.9631676E-02 0.6248438 at 90iterations 1.0019390E-02 0.2771244 at 100iterations 5.1336666E-03 0.1604061 at 110iterations 2.6904689E-03 9.1529846E-02 at 120iterations finished qdiffx linear iterations at : 06:12:25 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 2.6904689E-03 9.1529846E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 06:12:26 7.515u 0.228s 0:08.06 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 Tue Oct 11 2011 at 06:12:26 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: SEP 190 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.250680 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): 0.8059999 46.23500 ymin,ymax (A): 0.6860000 40.29500 zmin,zma (A): -2.093000 47.18900 x,y,z range (A): 45.42900 39.60900 49.28200 scale (grids/A): 3.250680 object centre (A): 23.52050 20.49050 22.54800 number of atom coordinates read : 2061 total number of charged atoms : 1931 net assigned charge : 7.025009 assigned positive charge : 314.5471 centred at (gu) : 95.63209 92.60770 91.20237 assigned negative charge : -307.5222 centred at (gu) : 96.48058 92.48689 91.35149 start vw surface at 0.1300000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 179398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16968 grid for indexing accessible points = 1.400000 m= 98955 mr = 133717 m= 41300 mr = 82932 m= 12303 mr = 34291 m= 2648 mr = 9689 m= 297 mr = 1929 m= 11 mr = 189 m= 0 mr = 5 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 72160 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 15448 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) : 2.167120 object centre at (A) : 23.52050 20.49050 22.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4009043 0.8288999 midg,1,midg; midg,igrid,midg -4.9864710E-04 0.2867441 1,midg,midg; igrid,midg,midg 0.2966025 0.1046087 gauss-seidel spectral radius is 0.9993056 estimated iterations to convergence 299 setup time was (sec) 2.110000 now iterating at: 06:12:28 rms-change max change #iterations 10.52899 330.3880 at 10iterations 6.257011 133.2334 at 20iterations 3.707028 80.75806 at 30iterations 2.192409 42.57167 at 40iterations 1.295528 25.98703 at 50iterations 0.7624959 13.75436 at 60iterations 0.4499244 9.010603 at 70iterations 0.2644453 4.514452 at 80iterations 0.1562818 2.683025 at 90iterations 9.1687202E-02 1.606352 at 100iterations 5.4228310E-02 0.9809246 at 110iterations 3.2015357E-02 0.5387115 at 120iterations 1.9103544E-02 0.3422775 at 130iterations 1.1583225E-02 0.1973343 at 140iterations 7.2001466E-03 0.1300812 at 150iterations 4.6563246E-03 8.4993362E-02 at 160iterations 3.1797828E-03 5.3787231E-02 at 170iterations 2.3138069E-03 3.8238525E-02 at 180iterations finished qdiffx linear iterations at : 06:12:38 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 2.3138069E-03 3.8238525E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 06:12:39 12.375u 0.203s 0:13.17 95.4% 0+0k 0+0io 0pf+0w