Mon Oct 10 09:51:37 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 Mon Oct 10 2011 at 09:51:37 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 = 2810 !!! WARNING: HIT 232 has a net charge of 0.5140 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: 0.5790030 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): -16.97900 36.26600 ymin,ymax (A): -63.36300 -4.759000 zmin,zma (A): -4.210000 57.27500 x,y,z range (A): 53.24500 58.60400 61.48500 scale (grids/A): 0.5790030 object centre (A): 9.643499 -34.06100 26.53250 number of atom coordinates read : 2810 total number of charged atoms : 2661 net assigned charge : 7.014012 assigned positive charge : 416.4290 centred at (gu) : 88.99655 89.41989 87.60015 assigned negative charge : -409.4154 centred at (gu) : 89.11164 89.33755 87.48576 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6356 nv = 96 ne = 84 npr = 54256 no. pairs analyzed = 54256 no. exposed pairs = 4295 no. arc points = 30980 no. surface atoms = 1398 nbur = 1412 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 299 mr = 2748 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3105 ## 347 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3960489E-09 2.1330711E-09 midg,1,midg; midg,igrid,midg -1.2606327E-10 2.7105964E-09 1,midg,midg; igrid,midg,midg 4.7157567E-09 -5.7826938E-10 gauss-seidel spectral radius is 0.9846091 estimated iterations to convergence 66 setup time was (sec) 0.6500000 now iterating at: 09:51:38 rms-change max change #iterations 9.1242142E-02 16.03761 at 10iterations 7.2092684E-03 1.147400 at 20iterations 5.8157754E-04 0.1021519 at 30iterations 6.3412721E-05 8.5124969E-03 at 40iterations 1.1653847E-05 1.2454987E-03 at 50iterations finished qdiffx linear iterations at : 09:51:42 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.1653847E-05 1.2454987E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 09:51:42 4.249u 0.249s 0:04.84 92.5% 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 Mon Oct 10 2011 at 09:51:42 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2810 !!! WARNING: HIT 232 has a net charge of 0.5140 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: 1.737009 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): -16.97900 36.26600 ymin,ymax (A): -63.36300 -4.759000 zmin,zma (A): -4.210000 57.27500 x,y,z range (A): 53.24500 58.60400 61.48500 scale (grids/A): 1.737009 object centre (A): 9.643499 -34.06100 26.53250 number of atom coordinates read : 2810 total number of charged atoms : 2661 net assigned charge : 7.014012 assigned positive charge : 416.4290 centred at (gu) : 86.98907 88.25909 82.79990 assigned negative charge : -409.4154 centred at (gu) : 87.33447 88.01225 82.45687 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30980 grid for indexing accessible points = 1.400000 m= 21457 mr = 41884 m= 2688 mr = 13393 m= 123 mr = 1148 m= 0 mr = 13 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.5500000 number of dielectric boundary points 36328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 300 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 20660 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) : 0.5790030 object centre at (A) : 9.643499 -34.06100 26.53250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0917320E-04 1.3507674E-02 midg,1,midg; midg,igrid,midg 2.0312455E-02 3.5140011E-02 1,midg,midg; igrid,midg,midg 1.7630097E-02 -8.7713171E-04 gauss-seidel spectral radius is 0.9984062 estimated iterations to convergence 199 setup time was (sec) 0.8700000 now iterating at: 09:51:43 rms-change max change #iterations 3.634483 161.3100 at 10iterations 1.594072 61.95613 at 20iterations 0.6992748 24.16898 at 30iterations 0.3068544 10.28223 at 40iterations 0.1346987 5.271046 at 50iterations 5.9496708E-02 2.078903 at 60iterations 2.5953688E-02 0.8939452 at 70iterations 1.1474055E-02 0.4190941 at 80iterations 5.0226436E-03 0.1895041 at 90iterations 2.2221247E-03 7.7680498E-02 at 100iterations 9.7125157E-04 3.4027100E-02 at 110iterations 4.2676931E-04 1.5046477E-02 at 120iterations finished qdiffx linear iterations at : 09:51:52 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 4.2676931E-04 1.5046477E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 09:51:53 9.593u 0.243s 0:10.34 95.0% 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 Mon Oct 10 2011 at 09:51:53 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 = 2810 !!! WARNING: HIT 232 has a net charge of 0.5140 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: 2.605514 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): -16.97900 36.26600 ymin,ymax (A): -63.36300 -4.759000 zmin,zma (A): -4.210000 57.27500 x,y,z range (A): 53.24500 58.60400 61.48500 scale (grids/A): 2.605514 object centre (A): 9.643499 -34.06100 26.53250 number of atom coordinates read : 2810 total number of charged atoms : 2661 net assigned charge : 7.014012 assigned positive charge : 416.4290 centred at (gu) : 85.48346 87.38857 79.19983 assigned negative charge : -409.4154 centred at (gu) : 86.00163 87.01829 78.68527 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 158371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30980 grid for indexing accessible points = 1.400000 m= 70491 mr = 103450 m= 22079 mr = 52189 m= 4182 mr = 15475 m= 433 mr = 2336 m= 15 mr = 194 m= 0 mr = 3 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 1.400000 number of dielectric boundary points 81924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 21281 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) : 1.737009 object centre at (A) : 9.643499 -34.06100 26.53250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3848183E-02 0.2214128 midg,1,midg; midg,igrid,midg 0.5583093 0.5003752 1,midg,midg; igrid,midg,midg 0.1802081 1.6258555E-02 gauss-seidel spectral radius is 0.9992206 estimated iterations to convergence 283 setup time was (sec) 1.750000 now iterating at: 09:51:55 rms-change max change #iterations 9.284297 313.5117 at 10iterations 5.463979 168.3464 at 20iterations 3.174138 77.11855 at 30iterations 1.831527 42.84031 at 40iterations 1.051371 27.12440 at 50iterations 0.6022846 15.02229 at 60iterations 0.3439946 8.383866 at 70iterations 0.1965204 4.281991 at 80iterations 0.1115783 2.542777 at 90iterations 6.3644283E-02 1.440613 at 100iterations 3.6176205E-02 0.8158455 at 110iterations 2.0519322E-02 0.4258275 at 120iterations 1.1619633E-02 0.2297726 at 130iterations 6.5901848E-03 0.1325302 at 140iterations 3.7343267E-03 7.6627731E-02 at 150iterations 2.1200120E-03 4.6409607E-02 at 160iterations 1.2016102E-03 2.7753830E-02 at 170iterations 6.8028551E-04 1.4572144E-02 at 180iterations finished qdiffx linear iterations at : 09:52:08 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 6.8028551E-04 1.4572144E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.58000 DelPhi exited at 09:52:09 15.586u 0.275s 0:16.16 98.0% 0+0k 0+0io 0pf+0w