Tue Oct 11 06:43:32 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 06:43:32 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7067840 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): 2.387000 47.52900 ymin,ymax (A): 0.6240000 40.52400 zmin,zma (A): -3.370000 46.99900 x,y,z range (A): 45.14200 39.90000 50.36900 scale (grids/A): 0.7067840 object centre (A): 24.95800 20.57400 21.81450 number of atom coordinates read : 2199 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 310.8071 centred at (gu) : 90.06432 90.57359 90.45755 assigned negative charge : -303.8762 centred at (gu) : 90.25373 90.55614 90.49185 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6914 nv = 96 ne = 84 npr = 39877 no. pairs analyzed = 39877 no. exposed pairs = 2480 no. arc points = 16988 no. surface atoms = 843 nbur = 1356 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 3954 m= 6 mr = 71 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 0.2700000 number of dielectric boundary points 3336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1592 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7614 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7816323E-08 4.5060148E-08 midg,1,midg; midg,igrid,midg 4.4468560E-08 7.3640422E-08 1,midg,midg; igrid,midg,midg 1.4414799E-07 -3.4338726E-08 gauss-seidel spectral radius is 0.9895608 estimated iterations to convergence 80 setup time was (sec) 0.5000000 now iterating at: 06:43:33 rms-change max change #iterations 0.1989401 29.65355 at 10iterations 2.5203589E-02 3.778181 at 20iterations 3.2113730E-03 0.5025463 at 30iterations 4.9703033E-04 6.3450813E-02 at 40iterations 1.0854155E-04 1.4724731E-02 at 50iterations finished qdiffx linear iterations at : 06:43:35 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.0854155E-04 1.4724731E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 06:43:36 3.349u 0.163s 0:04.00 87.5% 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 06:43:36 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.120352 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): 2.387000 47.52900 ymin,ymax (A): 0.6240000 40.52400 zmin,zma (A): -3.370000 46.99900 x,y,z range (A): 45.14200 39.90000 50.36900 scale (grids/A): 2.120352 object centre (A): 24.95800 20.57400 21.81450 number of atom coordinates read : 2199 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 310.8071 centred at (gu) : 90.19296 91.72074 91.37281 assigned negative charge : -303.8762 centred at (gu) : 90.76151 91.66859 91.47542 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16988 grid for indexing accessible points = 1.400000 m= 29265 mr = 52451 m= 5594 mr = 22091 m= 527 mr = 3735 m= 9 mr = 259 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 30610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15132 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) : 0.7067840 object centre at (A) : 24.95800 20.57400 21.81450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1409992E-02 6.6320039E-02 midg,1,midg; midg,igrid,midg 3.6473670E-03 3.1448781E-02 1,midg,midg; igrid,midg,midg 4.3797683E-02 9.7624501E-03 gauss-seidel spectral radius is 0.9988259 estimated iterations to convergence 231 setup time was (sec) 0.8600000 now iterating at: 06:43:37 rms-change max change #iterations 4.575536 195.4468 at 10iterations 2.259925 78.30656 at 20iterations 1.119241 37.01387 at 30iterations 0.5557734 16.81874 at 40iterations 0.2762165 8.829603 at 50iterations 0.1367585 4.123558 at 60iterations 6.7756854E-02 2.023380 at 70iterations 3.3875581E-02 1.117685 at 80iterations 1.6885463E-02 0.5195228 at 90iterations 8.4988922E-03 0.2722979 at 100iterations 4.2731147E-03 0.1460075 at 110iterations 2.1944526E-03 6.7029953E-02 at 120iterations finished qdiffx linear iterations at : 06:43:44 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 2.1944526E-03 6.7029953E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 06:43:44 7.650u 0.215s 0:08.28 94.9% 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 06:43:44 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.180528 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): 2.387000 47.52900 ymin,ymax (A): 0.6240000 40.52400 zmin,zma (A): -3.370000 46.99900 x,y,z range (A): 45.14200 39.90000 50.36900 scale (grids/A): 3.180528 object centre (A): 24.95800 20.57400 21.81450 number of atom coordinates read : 2199 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 310.8071 centred at (gu) : 90.28947 92.58105 92.05921 assigned negative charge : -303.8762 centred at (gu) : 91.14236 92.50297 92.21312 start vw surface at 0.1600000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 169906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16988 grid for indexing accessible points = 1.400000 m= 91904 mr = 126208 m= 36524 mr = 76278 m= 10617 mr = 29963 m= 2217 mr = 8198 m= 239 mr = 1604 m= 7 mr = 148 m= 0 mr = 4 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 69011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 15382 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) : 2.120352 object centre at (A) : 24.95800 20.57400 21.81450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3392135 0.6974793 midg,1,midg; midg,igrid,midg -3.2314518E-03 0.2414259 1,midg,midg; igrid,midg,midg 0.3288883 0.2200245 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 2.180000 now iterating at: 06:43:47 rms-change max change #iterations 10.16302 325.1837 at 10iterations 6.002131 140.2538 at 20iterations 3.537675 72.26939 at 30iterations 2.085481 38.35218 at 40iterations 1.226975 23.72199 at 50iterations 0.7202964 13.65879 at 60iterations 0.4225511 8.526890 at 70iterations 0.2475905 4.320642 at 80iterations 0.1447707 2.685562 at 90iterations 8.4878176E-02 1.618471 at 100iterations 4.9809519E-02 0.9654427 at 110iterations 2.9308662E-02 0.5384140 at 120iterations 1.7347706E-02 0.3270912 at 130iterations 1.0401189E-02 0.1946449 at 140iterations 6.3425270E-03 0.1302490 at 150iterations 3.9938777E-03 8.7310791E-02 at 160iterations 2.6368559E-03 5.6091309E-02 at 170iterations 1.8329088E-03 3.6346436E-02 at 180iterations finished qdiffx linear iterations at : 06:43:57 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 1.8329088E-03 3.6346436E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 06:43:58 12.798u 0.224s 0:13.50 96.3% 0+0k 0+0io 0pf+0w