Tue Oct 11 04:22:17 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 04:22:17 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6639932 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): -14.90500 29.32700 ymin,ymax (A): 7.561000 51.81800 zmin,zma (A): 25.47600 79.09100 x,y,z range (A): 44.23200 44.25700 53.61501 scale (grids/A): 0.6639932 object centre (A): 7.211000 29.68950 52.28350 number of atom coordinates read : 2565 total number of charged atoms : 2416 net assigned charge : 4.176023 assigned positive charge : 385.8499 centred at (gu) : 90.63667 91.00225 89.03717 assigned negative charge : -381.6745 centred at (gu) : 90.97549 90.76981 89.10957 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7616 nv = 96 ne = 84 npr = 52788 no. pairs analyzed = 52788 no. exposed pairs = 3060 no. arc points = 21177 no. surface atoms = 1027 nbur = 1538 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4431 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.2900000 number of dielectric boundary points 3572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2051 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8907 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3256551E-08 -3.0679856E-09 midg,1,midg; midg,igrid,midg -3.1815738E-08 7.4743120E-08 1,midg,midg; igrid,midg,midg 7.1887236E-08 -7.3058828E-08 gauss-seidel spectral radius is 0.9882365 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 04:22:18 rms-change max change #iterations 0.1745929 24.23890 at 10iterations 1.9075610E-02 2.530895 at 20iterations 2.1196271E-03 0.3066559 at 30iterations 2.7375735E-04 3.9566040E-02 at 40iterations 5.2520121E-05 6.3762665E-03 at 50iterations finished qdiffx linear iterations at : 04:22:21 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 5.2520121E-05 6.3762665E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 04:22:23 3.958u 0.421s 0:05.23 83.5% 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 04:22:23 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.991980 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): -14.90500 29.32700 ymin,ymax (A): 7.561000 51.81800 zmin,zma (A): 25.47600 79.09100 x,y,z range (A): 44.23200 44.25700 53.61501 scale (grids/A): 1.991980 object centre (A): 7.211000 29.68950 52.28350 number of atom coordinates read : 2565 total number of charged atoms : 2416 net assigned charge : 4.176023 assigned positive charge : 385.8499 centred at (gu) : 91.90941 93.00618 87.11102 assigned negative charge : -381.6745 centred at (gu) : 92.92645 92.30920 87.32838 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21177 grid for indexing accessible points = 1.400000 m= 31438 mr = 58792 m= 5382 mr = 23906 m= 382 mr = 3548 m= 5 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2445 time to turn everything in is 0.6500000 number of dielectric boundary points 32949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19107 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) : 0.6639932 object centre at (A) : 7.211000 29.68950 52.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1261657E-02 -1.0383182E-02 midg,1,midg; midg,igrid,midg -1.2601723E-02 4.4514768E-02 1,midg,midg; igrid,midg,midg 6.5963611E-02 -5.5932142E-02 gauss-seidel spectral radius is 0.9987408 estimated iterations to convergence 223 setup time was (sec) 0.9500000 now iterating at: 04:22:24 rms-change max change #iterations 4.636393 186.2716 at 10iterations 2.242488 73.42485 at 20iterations 1.082301 35.45734 at 30iterations 0.5218981 15.46813 at 40iterations 0.2534517 8.572563 at 50iterations 0.1223842 3.619776 at 60iterations 5.9169024E-02 1.851745 at 70iterations 2.8578913E-02 0.9148317 at 80iterations 1.3829978E-02 0.3896399 at 90iterations 6.6819689E-03 0.1850281 at 100iterations 3.2525097E-03 0.1058598 at 110iterations 1.5782312E-03 4.7363281E-02 at 120iterations finished qdiffx linear iterations at : 04:22:33 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.5782312E-03 4.7363281E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 04:22:33 9.612u 0.453s 0:10.49 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 04:22:33 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.987969 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): -14.90500 29.32700 ymin,ymax (A): 7.561000 51.81800 zmin,zma (A): 25.47600 79.09100 x,y,z range (A): 44.23200 44.25700 53.61501 scale (grids/A): 2.987969 object centre (A): 7.211000 29.68950 52.28350 number of atom coordinates read : 2565 total number of charged atoms : 2416 net assigned charge : 4.176023 assigned positive charge : 385.8499 centred at (gu) : 92.86393 94.50917 85.66649 assigned negative charge : -381.6745 centred at (gu) : 94.38951 93.46360 85.99247 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 189920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21177 grid for indexing accessible points = 1.400000 m= 100356 mr = 141895 m= 38195 mr = 83718 m= 9839 mr = 31330 m= 1611 mr = 7657 m= 106 mr = 1107 m= 5 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 8830 time to turn everything in is 1.730000 number of dielectric boundary points 74262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 19317 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) : 1.991980 object centre at (A) : 7.211000 29.68950 52.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4307017 -1.3480433E-02 midg,1,midg; midg,igrid,midg -0.1287760 0.3562573 1,midg,midg; igrid,midg,midg 0.5622274 -0.6002622 gauss-seidel spectral radius is 0.9992796 estimated iterations to convergence 294 setup time was (sec) 2.140000 now iterating at: 04:22:36 rms-change max change #iterations 10.51329 442.5229 at 10iterations 6.162945 129.9582 at 20iterations 3.614076 64.76219 at 30iterations 2.112501 40.58281 at 40iterations 1.231864 24.99656 at 50iterations 0.7180781 12.23259 at 60iterations 0.4181435 7.267123 at 70iterations 0.2434221 4.650030 at 80iterations 0.1417318 2.853489 at 90iterations 8.2305759E-02 1.344864 at 100iterations 4.7815956E-02 0.8774643 at 110iterations 2.7812410E-02 0.4688066 at 120iterations 1.6211685E-02 0.2755795 at 130iterations 9.4545865E-03 0.1573372 at 140iterations 5.5421311E-03 0.1104126 at 150iterations 3.2776576E-03 6.2377930E-02 at 160iterations 1.9669475E-03 3.3796310E-02 at 170iterations 1.2096051E-03 2.5789261E-02 at 180iterations finished qdiffx linear iterations at : 04:22:50 total time elapsed so far: 16.41000 # loops : 180 mean,max change (kT/e) : 1.2096051E-03 2.5789261E-02 energy calculations done at 16.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.58000 DelPhi exited at 04:22:50 16.589u 0.458s 0:17.35 98.1% 0+0k 0+0io 0pf+0w