Mon Oct 10 17:09:42 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 Mon Oct 10 2011 at 17:09:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5943140 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): -6.454000 53.44700 ymin,ymax (A): 5.272000 58.69900 zmin,zma (A): 71.33300 124.9600 x,y,z range (A): 59.90100 53.42700 53.62700 scale (grids/A): 0.5943140 object centre (A): 23.49650 31.98550 98.14650 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 5.500041 assigned positive charge : 484.4078 centred at (gu) : 90.06686 90.06387 90.58463 assigned negative charge : -478.9093 centred at (gu) : 90.02519 90.07520 90.63394 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7398 nv = 96 ne = 84 npr = 64066 no. pairs analyzed = 64066 no. exposed pairs = 4509 no. arc points = 31941 no. surface atoms = 1484 nbur = 1719 mkacc time = 0.1100000 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 = 1.456000 m= 423 mr = 3512 m= 8 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2400000 number of dielectric boundary points 4277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3152 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9344 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3422733E-09 9.5269452E-11 midg,1,midg; midg,igrid,midg 2.3593580E-09 1.5605713E-09 1,midg,midg; igrid,midg,midg 3.8333647E-10 3.5842942E-09 gauss-seidel spectral radius is 0.9854080 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 17:09:42 rms-change max change #iterations 0.1170566 18.18219 at 10iterations 9.3647651E-03 1.493736 at 20iterations 8.0400985E-04 0.1305695 at 30iterations 6.6572415E-05 1.1188507E-02 at 40iterations 5.9920280E-06 9.3871355E-04 at 50iterations finished qdiffx linear iterations at : 17:09:45 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 5.9920280E-06 9.3871355E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 17:09:46 3.428u 0.161s 0:04.07 87.9% 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 Mon Oct 10 2011 at 17:09:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.782942 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): -6.454000 53.44700 ymin,ymax (A): 5.272000 58.69900 zmin,zma (A): 71.33300 124.9600 x,y,z range (A): 59.90100 53.42700 53.62700 scale (grids/A): 1.782942 object centre (A): 23.49650 31.98550 98.14650 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 5.500041 assigned positive charge : 484.4078 centred at (gu) : 90.19960 90.19069 91.75335 assigned negative charge : -478.9093 centred at (gu) : 90.07565 90.22538 91.90161 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31941 grid for indexing accessible points = 1.400000 m= 26906 mr = 50230 m= 4159 mr = 17882 m= 232 mr = 2177 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 158 time to turn everything in is 0.3900000 number of dielectric boundary points 39608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23839 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) : 0.5943140 object centre at (A) : 23.49650 31.98550 98.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6902402E-03 -6.8403390E-04 midg,1,midg; midg,igrid,midg 1.1736363E-02 1.6668893E-03 1,midg,midg; igrid,midg,midg 3.7720564E-03 2.4034971E-02 gauss-seidel spectral radius is 0.9985280 estimated iterations to convergence 207 setup time was (sec) 0.6100000 now iterating at: 17:09:47 rms-change max change #iterations 4.186363 172.5939 at 10iterations 1.888240 72.22305 at 20iterations 0.8586984 30.51698 at 30iterations 0.3883395 14.04439 at 40iterations 0.1763359 5.841131 at 50iterations 8.0142088E-02 2.739141 at 60iterations 3.6258213E-02 1.103639 at 70iterations 1.6505308E-02 0.5162163 at 80iterations 7.5070700E-03 0.2453763 at 90iterations 3.4156020E-03 0.1025925 at 100iterations 1.5673155E-03 5.0676823E-02 at 110iterations 7.1964529E-04 2.3864031E-02 at 120iterations finished qdiffx linear iterations at : 17:09:54 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 7.1964529E-04 2.3864031E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 17:09:54 7.859u 0.198s 0:08.47 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 Mon Oct 10 2011 at 17:09:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.674413 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): -6.454000 53.44700 ymin,ymax (A): 5.272000 58.69900 zmin,zma (A): 71.33300 124.9600 x,y,z range (A): 59.90100 53.42700 53.62700 scale (grids/A): 2.674413 object centre (A): 23.49650 31.98550 98.14650 number of atom coordinates read : 3203 total number of charged atoms : 3059 net assigned charge : 5.500041 assigned positive charge : 484.4078 centred at (gu) : 90.29922 90.28569 92.62955 assigned negative charge : -478.9093 centred at (gu) : 90.11347 90.33817 92.85233 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 181533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31941 grid for indexing accessible points = 1.400000 m= 86240 mr = 122964 m= 30686 mr = 65915 m= 7010 mr = 22924 m= 829 mr = 4610 m= 29 mr = 422 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 511 time to turn everything in is 0.9900000 number of dielectric boundary points 89489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 24468 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) : 1.782942 object centre at (A) : 23.49650 31.98550 98.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0714653E-03 -7.9146279E-03 midg,1,midg; midg,igrid,midg 0.1888780 8.7641478E-02 1,midg,midg; igrid,midg,midg 2.9607201E-02 0.2645185 gauss-seidel spectral radius is 0.9992576 estimated iterations to convergence 290 setup time was (sec) 1.230000 now iterating at: 17:09:56 rms-change max change #iterations 10.43813 289.5930 at 10iterations 6.220282 129.2323 at 20iterations 3.659992 86.46699 at 30iterations 2.143008 46.13726 at 40iterations 1.253058 25.77855 at 50iterations 0.7257555 16.54584 at 60iterations 0.4209300 8.887722 at 70iterations 0.2436508 4.949884 at 80iterations 0.1408886 2.611526 at 90iterations 8.1081450E-02 1.559268 at 100iterations 4.6605922E-02 0.8700867 at 110iterations 2.6889300E-02 0.5095205 at 120iterations 1.5449069E-02 0.2867966 at 130iterations 8.8876653E-03 0.1900584 at 140iterations 5.1202020E-03 9.0438843E-02 at 150iterations 2.9312549E-03 5.5191278E-02 at 160iterations 1.6888002E-03 2.9919624E-02 at 170iterations 9.6832705E-04 1.8576622E-02 at 180iterations finished qdiffx linear iterations at : 17:10:07 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 9.6832705E-04 1.8576622E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 17:10:08 12.969u 0.214s 0:13.59 96.9% 0+0k 0+0io 0pf+0w