Tue Nov 22 14:11:00 PST 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 Nov 22 2011 at 14:11:04 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5826895 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): -25.27900 35.81700 ymin,ymax (A): -18.90000 20.49900 zmin,zma (A): -3.436000 38.61100 x,y,z range (A): 61.09600 39.39900 42.04700 scale (grids/A): 0.5826895 object centre (A): 5.269001 0.7995005 17.58750 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.77563 90.24984 90.55647 assigned negative charge : -284.8263 centred at (gu) : 89.79115 90.33178 90.67539 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4458 nv = 96 ne = 84 npr = 40156 no. pairs analyzed = 40156 no. exposed pairs = 2421 no. arc points = 17343 no. surface atoms = 817 nbur = 1147 mkacc time = 8.0000006E-02 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 = 1.484000 m= 173 mr = 2406 m= 0 mr = 12 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1797 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5541 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2340885E-09 -1.2887645E-09 midg,1,midg; midg,igrid,midg 1.8747635E-09 -5.7521549E-10 1,midg,midg; igrid,midg,midg 1.0262122E-09 4.7213866E-10 gauss-seidel spectral radius is 0.9847126 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 14:11:08 rms-change max change #iterations 7.8647129E-02 14.33153 at 10iterations 6.2583494E-03 1.069478 at 20iterations 4.9296598E-04 8.6346626E-02 at 30iterations 3.7547863E-05 6.0644150E-03 at 40iterations 3.0279884E-06 5.6552887E-04 at 50iterations finished qdiffx linear iterations at : 14:11:15 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 3.0279884E-06 5.6552887E-04 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 14:11:18 3.177u 0.169s 0:14.76 22.5% 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 Nov 22 2011 at 14:11:21 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.748069 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): -25.27900 35.81700 ymin,ymax (A): -18.90000 20.49900 zmin,zma (A): -3.436000 38.61100 x,y,z range (A): 61.09600 39.39900 42.04700 scale (grids/A): 1.748069 object centre (A): 5.269001 0.7995005 17.58750 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.32703 90.74948 91.66967 assigned negative charge : -284.8263 centred at (gu) : 89.37383 90.99559 92.02643 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 48585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17343 grid for indexing accessible points = 1.400000 m= 16487 mr = 33102 m= 1895 mr = 12345 m= 33 mr = 1121 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2800 time to turn everything in is 0.3200000 number of dielectric boundary points 20427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 14189 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) : 0.5826895 object centre at (A) : 5.269001 0.7995005 17.58750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9607634E-03 -5.7782000E-03 midg,1,midg; midg,igrid,midg 3.1045093E-03 -1.4976226E-03 1,midg,midg; igrid,midg,midg 3.5034996E-02 2.2866003E-02 gauss-seidel spectral radius is 0.9983021 estimated iterations to convergence 193 setup time was (sec) 0.5700000 now iterating at: 14:11:25 rms-change max change #iterations 3.000357 160.6567 at 10iterations 1.282823 55.11207 at 20iterations 0.5510005 22.84291 at 30iterations 0.2360806 9.389485 at 40iterations 0.1010346 4.133832 at 50iterations 4.3581288E-02 1.823822 at 60iterations 1.8630683E-02 0.8391013 at 70iterations 7.9859393E-03 0.3141513 at 80iterations 3.4269933E-03 0.1357908 at 90iterations 1.4621436E-03 5.9722900E-02 at 100iterations 6.2748924E-04 2.3742676E-02 at 110iterations 2.7015572E-04 1.0829926E-02 at 120iterations finished qdiffx linear iterations at : 14:11:44 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 2.7015572E-04 1.0829926E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 14:11:48 6.914u 0.167s 0:27.86 25.3% 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 Nov 22 2011 at 14:11:52 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.622103 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): -25.27900 35.81700 ymin,ymax (A): -18.90000 20.49900 zmin,zma (A): -3.436000 38.61100 x,y,z range (A): 61.09600 39.39900 42.04700 scale (grids/A): 2.622103 object centre (A): 5.269001 0.7995005 17.58750 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 88.99054 91.12412 92.50452 assigned negative charge : -284.8263 centred at (gu) : 89.06068 91.49342 93.03976 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 112527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17343 grid for indexing accessible points = 1.400000 m= 55412 mr = 80339 m= 17559 mr = 45681 m= 3033 mr = 14276 m= 172 mr = 2238 m= 4 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 9310 time to turn everything in is 0.8100000 number of dielectric boundary points 46078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14647 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) : 1.748069 object centre at (A) : 5.269001 0.7995005 17.58750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8784477E-02 -6.0226552E-02 midg,1,midg; midg,igrid,midg 2.5769101E-02 -1.9096769E-02 1,midg,midg; igrid,midg,midg 0.4111529 0.2577465 gauss-seidel spectral radius is 0.9991425 estimated iterations to convergence 270 setup time was (sec) 1.070000 now iterating at: 14:11:58 rms-change max change #iterations 7.317034 244.0471 at 10iterations 4.042773 115.1561 at 20iterations 2.229413 51.69911 at 30iterations 1.224918 30.36515 at 40iterations 0.6760035 15.84652 at 50iterations 0.3702793 8.795544 at 60iterations 0.2025248 4.931561 at 70iterations 0.1113043 2.606350 at 80iterations 6.1103627E-02 1.333525 at 90iterations 3.3548284E-02 0.8208675 at 100iterations 1.8364521E-02 0.4122944 at 110iterations 1.0058907E-02 0.2292106 at 120iterations 5.5261096E-03 0.1392727 at 130iterations 3.0354382E-03 6.5841675E-02 at 140iterations 1.6674658E-03 3.6067486E-02 at 150iterations 9.1659743E-04 1.9722939E-02 at 160iterations 5.0454953E-04 1.2167931E-02 at 170iterations 2.7623470E-04 5.9738159E-03 at 180iterations finished qdiffx linear iterations at : 14:12:27 total time elapsed so far: 10.63000 # loops : 180 mean,max change (kT/e) : 2.7623470E-04 5.9738159E-03 energy calculations done at 10.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 14:12:31 10.799u 0.176s 0:40.07 27.3% 0+0k 0+0io 0pf+0w