Sun Oct 9 20:03:08 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 Sun Oct 9 2011 at 20:03:08 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5622591 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): 2.929000 65.76300 ymin,ymax (A): -7.745000 54.67200 zmin,zma (A): -1.172000 62.14400 x,y,z range (A): 62.83400 62.41700 63.31600 scale (grids/A): 0.5622591 object centre (A): 34.34600 23.46350 30.48600 number of atom coordinates read : 5005 total number of charged atoms : 4857 net assigned charge : 1.621040 assigned positive charge : 767.7430 centred at (gu) : 87.79522 88.82762 88.94415 assigned negative charge : -766.1275 centred at (gu) : 87.68187 88.81364 88.94126 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10281 nv = 96 ne = 84 npr = 101646 no. pairs analyzed = 101646 no. exposed pairs = 5832 no. arc points = 39201 no. surface atoms = 1975 nbur = 3030 mkacc time = 0.1800000 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 = 1.540000 m= 447 mr = 5892 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4002 ## 406 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13472 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4290356E-10 2.3988175E-10 midg,1,midg; midg,igrid,midg -5.4459996E-11 4.0386933E-10 1,midg,midg; igrid,midg,midg -3.6523329E-09 1.4924570E-09 gauss-seidel spectral radius is 0.9838307 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 20:03:08 rms-change max change #iterations 0.1158474 15.45037 at 10iterations 1.1196541E-02 1.341995 at 20iterations 3.5122654E-03 0.3842163 at 30iterations 1.7034077E-03 0.2074986 at 40iterations 8.5091533E-04 0.1075916 at 50iterations finished qdiffx linear iterations at : 20:03:11 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 8.5091533E-04 0.1075916 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 20:03:12 3.501u 0.146s 0:03.93 92.6% 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 Sun Oct 9 2011 at 20:03:12 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.686777 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): 2.929000 65.76300 ymin,ymax (A): -7.745000 54.67200 zmin,zma (A): -1.172000 62.14400 x,y,z range (A): 62.83400 62.41700 63.31600 scale (grids/A): 1.686777 object centre (A): 34.34600 23.46350 30.48600 number of atom coordinates read : 5005 total number of charged atoms : 4857 net assigned charge : 1.621040 assigned positive charge : 767.7430 centred at (gu) : 83.38440 86.48167 86.83096 assigned negative charge : -766.1275 centred at (gu) : 83.04560 86.44090 86.82367 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 114608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39201 grid for indexing accessible points = 1.400000 m= 41132 mr = 83387 m= 5283 mr = 29971 m= 186 mr = 2928 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 249 time to turn everything in is 0.5300000 number of dielectric boundary points 44892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 37415 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) : 0.5622591 object centre at (A) : 34.34600 23.46350 30.48600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9324710E-02 -2.9916499E-02 midg,1,midg; midg,igrid,midg 1.5678078E-02 1.2704536E-02 1,midg,midg; igrid,midg,midg -2.2502234E-02 4.2215768E-02 gauss-seidel spectral radius is 0.9984831 estimated iterations to convergence 204 setup time was (sec) 0.7400000 now iterating at: 20:03:13 rms-change max change #iterations 4.925002 186.3793 at 10iterations 2.210019 60.41818 at 20iterations 0.9961871 29.04222 at 30iterations 0.4487699 11.82474 at 40iterations 0.2030499 5.794731 at 50iterations 9.1851205E-02 2.713840 at 60iterations 4.1975308E-02 1.158295 at 70iterations 1.9661387E-02 0.5416107 at 80iterations 9.9156415E-03 0.2830200 at 90iterations 5.6098811E-03 0.1666260 at 100iterations 3.6561077E-03 0.1010323 at 110iterations 2.6506807E-03 7.4264526E-02 at 120iterations finished qdiffx linear iterations at : 20:03:20 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.6506807E-03 7.4264526E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 20:03:20 7.969u 0.213s 0:08.53 95.7% 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 Sun Oct 9 2011 at 20:03:20 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.530166 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): 2.929000 65.76300 ymin,ymax (A): -7.745000 54.67200 zmin,zma (A): -1.172000 62.14400 x,y,z range (A): 62.83400 62.41700 63.31600 scale (grids/A): 2.530166 object centre (A): 34.34600 23.46350 30.48600 number of atom coordinates read : 5005 total number of charged atoms : 4857 net assigned charge : 1.621040 assigned positive charge : 767.7430 centred at (gu) : 80.07616 84.72197 85.24616 assigned negative charge : -766.1275 centred at (gu) : 79.56844 84.66137 85.23545 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 265907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39201 grid for indexing accessible points = 1.400000 m= 136456 mr = 201694 m= 45300 mr = 112056 m= 8726 mr = 35652 m= 834 mr = 6087 m= 17 mr = 468 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 762 time to turn everything in is 1.400000 number of dielectric boundary points 101283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 38829 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) : 1.686777 object centre at (A) : 34.34600 23.46350 30.48600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5497653 -0.7578518 midg,1,midg; midg,igrid,midg -2.0901997E-02 7.8731753E-02 1,midg,midg; igrid,midg,midg -0.4595978 0.7393401 gauss-seidel spectral radius is 0.9992629 estimated iterations to convergence 291 setup time was (sec) 1.650000 now iterating at: 20:03:22 rms-change max change #iterations 12.34991 348.4171 at 10iterations 7.309350 147.7809 at 20iterations 4.291538 86.16254 at 30iterations 2.516329 46.10544 at 40iterations 1.465635 24.73738 at 50iterations 0.8533861 14.36617 at 60iterations 0.4955870 7.666821 at 70iterations 0.2876701 4.491322 at 80iterations 0.1666942 2.954796 at 90iterations 9.6385419E-02 1.449602 at 100iterations 5.5914428E-02 0.9221458 at 110iterations 3.2615483E-02 0.5074196 at 120iterations 1.9248474E-02 0.3144836 at 130iterations 1.1567798E-02 0.1933441 at 140iterations 7.2674318E-03 0.1266670 at 150iterations 4.8450921E-03 8.4125519E-02 at 160iterations 3.4914401E-03 6.5807343E-02 at 170iterations 2.7022767E-03 4.3583393E-02 at 180iterations finished qdiffx linear iterations at : 20:03:34 total time elapsed so far: 13.60000 # loops : 180 mean,max change (kT/e) : 2.7022767E-03 4.3583393E-02 energy calculations done at 13.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 20:03:34 13.744u 0.205s 0:14.24 97.8% 0+0k 0+0io 0pf+0w