Mon Oct 10 17:02:19 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 17:02:19 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: WAT 5 has a net charge of -0.8340 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: 0.6062980 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): 13.43500 71.38200 ymin,ymax (A): 3.795000 50.90300 zmin,zma (A): 7.536000 66.25300 x,y,z range (A): 57.94701 47.10800 58.71700 scale (grids/A): 0.6062980 object centre (A): 42.40850 27.34900 36.89450 number of atom coordinates read : 2989 total number of charged atoms : 2838 net assigned charge : -4.319963 assigned positive charge : 451.7249 centred at (gu) : 89.30172 90.43577 90.43124 assigned negative charge : -456.0461 centred at (gu) : 89.16470 90.53184 90.55575 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7317 nv = 96 ne = 84 npr = 59883 no. pairs analyzed = 59883 no. exposed pairs = 3870 no. arc points = 27516 no. surface atoms = 1309 nbur = 1680 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3822 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2759 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9069 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8290726E-09 -9.6010080E-09 midg,1,midg; midg,igrid,midg 2.5203684E-09 -7.9354656E-09 1,midg,midg; igrid,midg,midg -1.0990381E-08 4.1357753E-09 gauss-seidel spectral radius is 0.9859571 estimated iterations to convergence 69 setup time was (sec) 0.4600000 now iterating at: 17:02:20 rms-change max change #iterations 0.1243949 20.31147 at 10iterations 1.0962972E-02 1.437936 at 20iterations 9.6022926E-04 0.1587067 at 30iterations 8.4076535E-05 1.1703491E-02 at 40iterations 7.3890646E-06 9.4604492E-04 at 50iterations finished qdiffx linear iterations at : 17:02:23 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 7.3890646E-06 9.4604492E-04 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 17:02:24 3.900u 0.234s 0:04.75 86.9% 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 17:02:24 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: WAT 5 has a net charge of -0.8340 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: 1.818894 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): 13.43500 71.38200 ymin,ymax (A): 3.795000 50.90300 zmin,zma (A): 7.536000 66.25300 x,y,z range (A): 57.94701 47.10800 58.71700 scale (grids/A): 1.818894 object centre (A): 42.40850 27.34900 36.89450 number of atom coordinates read : 2989 total number of charged atoms : 2838 net assigned charge : -4.319963 assigned positive charge : 451.7249 centred at (gu) : 87.90433 91.30636 91.29285 assigned negative charge : -456.0461 centred at (gu) : 87.49372 91.59505 91.66692 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27516 grid for indexing accessible points = 1.400000 m= 26161 mr = 53842 m= 3256 mr = 18431 m= 135 mr = 1759 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 660 time to turn everything in is 0.3800000 number of dielectric boundary points 35301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 22204 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) : 0.6062980 object centre at (A) : 42.40850 27.34900 36.89450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4013876E-02 -4.5521485E-04 midg,1,midg; midg,igrid,midg 1.3630850E-04 -2.4188429E-02 1,midg,midg; igrid,midg,midg -4.2632211E-02 2.7893402E-02 gauss-seidel spectral radius is 0.9985522 estimated iterations to convergence 208 setup time was (sec) 0.6100000 now iterating at: 17:02:25 rms-change max change #iterations 4.274865 191.0042 at 10iterations 1.950383 68.63707 at 20iterations 0.8883019 27.58041 at 30iterations 0.4063115 14.39143 at 40iterations 0.1860386 6.140915 at 50iterations 8.4797651E-02 2.631781 at 60iterations 3.8679816E-02 1.277598 at 70iterations 1.7728798E-02 0.5424194 at 80iterations 8.1245862E-03 0.2714643 at 90iterations 3.7326331E-03 0.1202097 at 100iterations 1.7001975E-03 5.1426888E-02 at 110iterations 7.8055600E-04 2.6664734E-02 at 120iterations finished qdiffx linear iterations at : 17:02:33 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 7.8055600E-04 2.6664734E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 17:02:33 8.376u 0.194s 0:09.01 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 17:02:33 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2989 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: WAT 5 has a net charge of -0.8340 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: 2.728341 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): 13.43500 71.38200 ymin,ymax (A): 3.795000 50.90300 zmin,zma (A): 7.536000 66.25300 x,y,z range (A): 57.94701 47.10800 58.71700 scale (grids/A): 2.728341 object centre (A): 42.40850 27.34900 36.89450 number of atom coordinates read : 2989 total number of charged atoms : 2838 net assigned charge : -4.319963 assigned positive charge : 451.7249 centred at (gu) : 86.85645 91.95917 91.93911 assigned negative charge : -456.0461 centred at (gu) : 86.24048 92.39246 92.50024 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27516 grid for indexing accessible points = 1.400000 m= 87654 mr = 130947 m= 28079 mr = 69996 m= 5399 mr = 21545 m= 573 mr = 3710 m= 29 mr = 361 m= 0 mr = 9 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 2214 time to turn everything in is 0.9900000 number of dielectric boundary points 79646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 22699 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) : 1.818894 object centre at (A) : 42.40850 27.34900 36.89450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1837530 0.1979109 midg,1,midg; midg,igrid,midg -1.2062047E-02 -0.2135026 1,midg,midg; igrid,midg,midg -0.4740114 0.4246405 gauss-seidel spectral radius is 0.9992555 estimated iterations to convergence 289 setup time was (sec) 1.250000 now iterating at: 17:02:35 rms-change max change #iterations 10.30268 315.6323 at 10iterations 6.046988 156.6901 at 20iterations 3.522179 78.16231 at 30iterations 2.038683 43.57445 at 40iterations 1.178601 26.64851 at 50iterations 0.6807038 13.99107 at 60iterations 0.3929352 7.616257 at 70iterations 0.2263211 3.996971 at 80iterations 0.1297530 2.417450 at 90iterations 7.4712001E-02 1.374472 at 100iterations 4.2883366E-02 0.8690853 at 110iterations 2.4621576E-02 0.4444008 at 120iterations 1.4132301E-02 0.2511067 at 130iterations 8.1042461E-03 0.1504822 at 140iterations 4.6550846E-03 8.6204529E-02 at 150iterations 2.6658089E-03 5.1439285E-02 at 160iterations 1.5326376E-03 2.6240349E-02 at 170iterations 8.7835744E-04 1.6496658E-02 at 180iterations finished qdiffx linear iterations at : 17:02:47 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 8.7835744E-04 1.6496658E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 17:02:48 13.467u 0.234s 0:14.19 96.4% 0+0k 0+0io 0pf+0w