Sun Oct 9 10:49:09 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 Sun Oct 9 2011 at 10:49:09 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 217 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5814713 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): -60.80100 0.4230000 ymin,ymax (A): -25.78200 32.00800 zmin,zma (A): -3.686000 53.50500 x,y,z range (A): 61.22400 57.79000 57.19100 scale (grids/A): 0.5814713 object centre (A): -30.18900 3.113000 24.90950 number of atom coordinates read : 3034 total number of charged atoms : 2891 net assigned charge : 5.514009 assigned positive charge : 445.8268 centred at (gu) : 89.68238 88.58497 92.01499 assigned negative charge : -440.3147 centred at (gu) : 89.67300 88.53971 91.99859 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6954 nv = 96 ne = 84 npr = 60268 no. pairs analyzed = 60268 no. exposed pairs = 4129 no. arc points = 29526 no. surface atoms = 1373 nbur = 1661 mkacc time = 0.1000000 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= 323 mr = 3497 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7532412E-10 2.6149694E-09 midg,1,midg; midg,igrid,midg 2.9804531E-10 1.6557421E-09 1,midg,midg; igrid,midg,midg 1.1321338E-09 1.3773069E-09 gauss-seidel spectral radius is 0.9847515 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 10:49:10 rms-change max change #iterations 0.1004887 18.03577 at 10iterations 7.8686476E-03 1.138296 at 20iterations 7.9950847E-04 0.1279678 at 30iterations 1.4544201E-04 2.3770809E-02 at 40iterations 3.8261151E-05 6.2607527E-03 at 50iterations finished qdiffx linear iterations at : 10:49:13 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.8261151E-05 6.2607527E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 10:49:13 3.381u 0.170s 0:03.85 92.2% 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 10:49:13 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 217 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.744414 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): -60.80100 0.4230000 ymin,ymax (A): -25.78200 32.00800 zmin,zma (A): -3.686000 53.50500 x,y,z range (A): 61.22400 57.79000 57.19100 scale (grids/A): 1.744414 object centre (A): -30.18900 3.113000 24.90950 number of atom coordinates read : 3034 total number of charged atoms : 2891 net assigned charge : 5.514009 assigned positive charge : 445.8268 centred at (gu) : 89.04617 85.75386 96.04401 assigned negative charge : -440.3147 centred at (gu) : 89.01885 85.61903 95.99570 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76467 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29526 grid for indexing accessible points = 1.400000 m= 24252 mr = 50945 m= 3362 mr = 16471 m= 164 mr = 1790 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 35010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 207 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 22484 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) : 0.5814713 object centre at (A) : -30.18900 3.113000 24.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0875857E-03 1.2561165E-02 midg,1,midg; midg,igrid,midg 2.1034623E-02 1.4371361E-02 1,midg,midg; igrid,midg,midg 9.8323226E-03 -7.2400658E-03 gauss-seidel spectral radius is 0.9984429 estimated iterations to convergence 201 setup time was (sec) 0.5800000 now iterating at: 10:49:14 rms-change max change #iterations 3.823025 183.1559 at 10iterations 1.682500 59.41734 at 20iterations 0.7472788 26.16004 at 30iterations 0.3315760 11.27378 at 40iterations 0.1478904 5.071381 at 50iterations 6.5700188E-02 2.063079 at 60iterations 2.9326044E-02 0.9430885 at 70iterations 1.3006143E-02 0.4748917 at 80iterations 5.8190860E-03 0.1906624 at 90iterations 2.6206374E-03 8.8653564E-02 at 100iterations 1.1860705E-03 3.7630081E-02 at 110iterations 5.4578058E-04 1.7766953E-02 at 120iterations finished qdiffx linear iterations at : 10:49:21 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 5.4578058E-04 1.7766953E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 10:49:21 7.734u 0.202s 0:08.28 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 10:49:22 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: HIR 217 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.616621 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): -60.80100 0.4230000 ymin,ymax (A): -25.78200 32.00800 zmin,zma (A): -3.686000 53.50500 x,y,z range (A): 61.22400 57.79000 57.19100 scale (grids/A): 2.616621 object centre (A): -30.18900 3.113000 24.90950 number of atom coordinates read : 3034 total number of charged atoms : 2891 net assigned charge : 5.514009 assigned positive charge : 445.8268 centred at (gu) : 88.56890 83.63041 99.06586 assigned negative charge : -440.3147 centred at (gu) : 88.52830 83.42848 98.99368 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 177810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29526 grid for indexing accessible points = 1.400000 m= 81282 mr = 125178 m= 26120 mr = 63293 m= 5392 mr = 19752 m= 577 mr = 3607 m= 20 mr = 323 m= 0 mr = 4 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 79044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 23119 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) : 1.744414 object centre at (A) : -30.18900 3.113000 24.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1592837E-02 0.2159188 midg,1,midg; midg,igrid,midg 0.4454816 0.1886605 1,midg,midg; igrid,midg,midg 0.1843680 -0.2081317 gauss-seidel spectral radius is 0.9992218 estimated iterations to convergence 283 setup time was (sec) 1.160000 now iterating at: 10:49:23 rms-change max change #iterations 9.573455 300.8743 at 10iterations 5.608443 163.1380 at 20iterations 3.245920 69.80293 at 30iterations 1.873293 43.70848 at 40iterations 1.076204 22.68112 at 50iterations 0.6167766 12.20665 at 60iterations 0.3520622 7.460796 at 70iterations 0.2004717 4.403573 at 80iterations 0.1141025 2.237286 at 90iterations 6.4999320E-02 1.201316 at 100iterations 3.6936361E-02 0.6965771 at 110iterations 2.1011757E-02 0.3845558 at 120iterations 1.1932631E-02 0.2115402 at 130iterations 6.7946669E-03 0.1281018 at 140iterations 3.8699352E-03 6.8374634E-02 at 150iterations 2.2147982E-03 4.2372704E-02 at 160iterations 1.2760358E-03 2.3773193E-02 at 170iterations 7.4366445E-04 1.4480591E-02 at 180iterations finished qdiffx linear iterations at : 10:49:34 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 7.4366445E-04 1.4480591E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 10:49:35 12.633u 0.214s 0:13.20 97.2% 0+0k 0+0io 0pf+0w