Tue Oct 11 03:46:42 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+sph.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 = amb.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 03:46:42 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: LYS 269 has a net charge of 0.2920 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6464382 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): -12.28400 36.96500 ymin,ymax (A): -27.03000 21.54800 zmin,zma (A): -9.637000 45.43400 x,y,z range (A): 49.24900 48.57800 55.07100 scale (grids/A): 0.6464382 object centre (A): 12.34050 -2.740999 17.89850 number of atom coordinates read : 2704 total number of charged atoms : 2552 net assigned charge : 4.454016 assigned positive charge : 406.5899 centred at (gu) : 90.36891 90.41763 91.77496 assigned negative charge : -402.1364 centred at (gu) : 90.14031 90.25527 91.79095 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7445 nv = 96 ne = 84 npr = 55872 no. pairs analyzed = 55872 no. exposed pairs = 3146 no. arc points = 21967 no. surface atoms = 1062 nbur = 1642 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 4288 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3600000 number of dielectric boundary points 3503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2196 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8979 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8894042E-09 7.6127247E-09 midg,1,midg; midg,igrid,midg -1.4637862E-08 3.3335287E-08 1,midg,midg; igrid,midg,midg -2.3941604E-08 4.2846800E-08 gauss-seidel spectral radius is 0.9876029 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 03:46:43 rms-change max change #iterations 0.1543636 21.27787 at 10iterations 1.5733996E-02 2.599400 at 20iterations 1.6443250E-03 0.2345943 at 30iterations 1.7966985E-04 2.4942398E-02 at 40iterations 2.6798223E-05 4.1017532E-03 at 50iterations finished qdiffx linear iterations at : 03:46:46 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 2.6798223E-05 4.1017532E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 03:46:46 3.686u 0.226s 0:04.32 90.2% 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 03:46:46 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: LYS 269 has a net charge of 0.2920 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.939315 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): -12.28400 36.96500 ymin,ymax (A): -27.03000 21.54800 zmin,zma (A): -9.637000 45.43400 x,y,z range (A): 49.24900 48.57800 55.07100 scale (grids/A): 1.939315 object centre (A): 12.34050 -2.740999 17.89850 number of atom coordinates read : 2704 total number of charged atoms : 2552 net assigned charge : 4.454016 assigned positive charge : 406.5899 centred at (gu) : 91.10609 91.25237 95.32427 assigned negative charge : -402.1364 centred at (gu) : 90.42062 90.76550 95.37244 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21967 grid for indexing accessible points = 1.400000 m= 30101 mr = 57429 m= 4707 mr = 22808 m= 288 mr = 2949 m= 7 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1167 time to turn everything in is 0.6300000 number of dielectric boundary points 32283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20124 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) : 0.6464382 object centre at (A) : 12.34050 -2.740999 17.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0620876E-02 1.5305507E-02 midg,1,midg; midg,igrid,midg -1.2599830E-02 2.9403305E-02 1,midg,midg; igrid,midg,midg -6.3493066E-03 5.0482288E-02 gauss-seidel spectral radius is 0.9986851 estimated iterations to convergence 218 setup time was (sec) 0.9400000 now iterating at: 03:46:47 rms-change max change #iterations 4.485910 180.4966 at 10iterations 2.137241 74.66315 at 20iterations 1.014871 33.88063 at 30iterations 0.4837613 14.91919 at 40iterations 0.2297908 6.776520 at 50iterations 0.1097593 3.045137 at 60iterations 5.2369364E-02 1.599682 at 70iterations 2.4869433E-02 0.8186026 at 80iterations 1.1823888E-02 0.3704147 at 90iterations 5.6446935E-03 0.1677513 at 100iterations 2.6964513E-03 9.0801239E-02 at 110iterations 1.2920210E-03 3.7406921E-02 at 120iterations finished qdiffx linear iterations at : 03:46:56 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 1.2920210E-03 3.7406921E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 03:46:56 9.373u 0.245s 0:10.14 94.7% 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 03:46:56 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: LYS 269 has a net charge of 0.2920 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.908972 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): -12.28400 36.96500 ymin,ymax (A): -27.03000 21.54800 zmin,zma (A): -9.637000 45.43400 x,y,z range (A): 49.24900 48.57800 55.07100 scale (grids/A): 2.908972 object centre (A): 12.34050 -2.740999 17.89850 number of atom coordinates read : 2704 total number of charged atoms : 2552 net assigned charge : 4.454016 assigned positive charge : 406.5899 centred at (gu) : 91.65911 91.87840 97.98635 assigned negative charge : -402.1364 centred at (gu) : 90.63087 91.14818 98.05850 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 185673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21967 grid for indexing accessible points = 1.400000 m= 97648 mr = 138291 m= 35610 mr = 81420 m= 8388 mr = 28990 m= 1256 mr = 6345 m= 88 mr = 866 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 3725 time to turn everything in is 1.560000 number of dielectric boundary points 72710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 20412 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) : 1.939315 object centre at (A) : 12.34050 -2.740999 17.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2590177 0.3576844 midg,1,midg; midg,igrid,midg -0.1623266 0.3507793 1,midg,midg; igrid,midg,midg -3.6808006E-02 0.4307722 gauss-seidel spectral radius is 0.9992674 estimated iterations to convergence 292 setup time was (sec) 1.880000 now iterating at: 03:46:59 rms-change max change #iterations 10.36842 387.4258 at 10iterations 6.067743 139.2453 at 20iterations 3.539354 77.21146 at 30iterations 2.054329 39.62641 at 40iterations 1.194449 24.65605 at 50iterations 0.6923820 13.22107 at 60iterations 0.4010023 7.042896 at 70iterations 0.2318056 4.098469 at 80iterations 0.1343219 2.775913 at 90iterations 7.7767156E-02 1.304483 at 100iterations 4.4841904E-02 0.7300901 at 110iterations 2.5896180E-02 0.5027294 at 120iterations 1.4941613E-02 0.2649298 at 130iterations 8.6396784E-03 0.1539187 at 140iterations 4.9828677E-03 8.5899353E-02 at 150iterations 2.8754803E-03 5.3804398E-02 at 160iterations 1.6614052E-03 3.0334473E-02 at 170iterations 9.5727068E-04 1.5930176E-02 at 180iterations finished qdiffx linear iterations at : 03:47:09 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 9.5727068E-04 1.5930176E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 03:47:11 13.058u 0.223s 0:14.07 94.3% 0+0k 0+0io 0pf+0w