Mon Oct 10 16:57:52 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 16:57:52 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2677 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: 0.5895699 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): 75.87200 124.9080 ymin,ymax (A): -10.40600 49.97700 zmin,zma (A): 119.2390 173.7940 x,y,z range (A): 49.03600 60.38300 54.55499 scale (grids/A): 0.5895699 object centre (A): 100.3900 19.78550 146.5165 number of atom coordinates read : 2677 total number of charged atoms : 2543 net assigned charge : 10.50002 assigned positive charge : 395.1785 centred at (gu) : 89.22044 89.07565 90.03114 assigned negative charge : -384.6794 centred at (gu) : 89.30332 88.97417 89.97604 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6243 nv = 96 ne = 84 npr = 53568 no. pairs analyzed = 53568 no. exposed pairs = 3394 no. arc points = 24141 no. surface atoms = 1146 nbur = 1531 mkacc time = 0.1200000 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= 293 mr = 3307 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2460 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7377441E-09 4.6471489E-09 midg,1,midg; midg,igrid,midg 6.0430722E-10 4.7002358E-09 1,midg,midg; igrid,midg,midg 6.3663688E-09 8.7009655E-10 gauss-seidel spectral radius is 0.9851273 estimated iterations to convergence 67 setup time was (sec) 0.5100000 now iterating at: 16:57:53 rms-change max change #iterations 9.9448614E-02 15.09176 at 10iterations 8.1392098E-03 1.336899 at 20iterations 6.8558671E-04 0.1063976 at 30iterations 7.1138777E-05 1.3813972E-02 at 40iterations 1.3248583E-05 3.1890869E-03 at 50iterations finished qdiffx linear iterations at : 16:57:56 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.3248583E-05 3.1890869E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 16:57:57 3.341u 0.164s 0:04.03 86.8% 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 16:57:57 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2677 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: 1.768710 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): 75.87200 124.9080 ymin,ymax (A): -10.40600 49.97700 zmin,zma (A): 119.2390 173.7940 x,y,z range (A): 49.03600 60.38300 54.55499 scale (grids/A): 1.768710 object centre (A): 100.3900 19.78550 146.5165 number of atom coordinates read : 2677 total number of charged atoms : 2543 net assigned charge : 10.50002 assigned positive charge : 395.1785 centred at (gu) : 87.66051 87.22637 90.09247 assigned negative charge : -384.6794 centred at (gu) : 87.90973 86.92231 89.92784 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24141 grid for indexing accessible points = 1.400000 m= 22742 mr = 46538 m= 2748 mr = 16161 m= 108 mr = 1324 m= 0 mr = 17 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 941 time to turn everything in is 0.5100000 number of dielectric boundary points 29864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19804 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) : 0.5895699 object centre at (A) : 100.3900 19.78550 146.5165 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6113967E-02 2.5169956E-02 midg,1,midg; midg,igrid,midg -1.6278246E-02 1.9856431E-03 1,midg,midg; igrid,midg,midg 1.1493427E-02 2.6110132E-04 gauss-seidel spectral radius is 0.9984331 estimated iterations to convergence 200 setup time was (sec) 0.7900000 now iterating at: 16:57:58 rms-change max change #iterations 3.646153 174.2493 at 10iterations 1.602607 60.27222 at 20iterations 0.7118326 26.25110 at 30iterations 0.3152392 11.31616 at 40iterations 0.1399523 4.527838 at 50iterations 6.1853498E-02 2.024230 at 60iterations 2.7535893E-02 0.9244804 at 70iterations 1.2144074E-02 0.4618235 at 80iterations 5.4203309E-03 0.2052823 at 90iterations 2.4012453E-03 8.2008362E-02 at 100iterations 1.0675160E-03 3.9750099E-02 at 110iterations 4.7616629E-04 1.8217087E-02 at 120iterations finished qdiffx linear iterations at : 16:58:04 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 4.7616629E-04 1.8217087E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 16:58:05 7.562u 0.207s 0:08.24 94.1% 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 16:58:05 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2677 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.653065 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): 75.87200 124.9080 ymin,ymax (A): -10.40600 49.97700 zmin,zma (A): 119.2390 173.7940 x,y,z range (A): 49.03600 60.38300 54.55499 scale (grids/A): 2.653065 object centre (A): 100.3900 19.78550 146.5165 number of atom coordinates read : 2677 total number of charged atoms : 2543 net assigned charge : 10.50002 assigned positive charge : 395.1785 centred at (gu) : 86.49052 85.83945 90.13840 assigned negative charge : -384.6794 centred at (gu) : 86.86442 85.38338 89.89171 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 158396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24141 grid for indexing accessible points = 1.400000 m= 75882 mr = 113393 m= 24113 mr = 60985 m= 4517 mr = 18444 m= 404 mr = 2971 m= 12 mr = 195 m= 0 mr = 1 time to grow re-entrant surface = 0.6600001 no. cavity mid-points inaccessible to solvent = 3331 time to turn everything in is 1.200000 number of dielectric boundary points 67335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 20338 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) : 1.768710 object centre at (A) : 100.3900 19.78550 146.5165 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1439092 0.2103090 midg,1,midg; midg,igrid,midg -0.3426481 4.6261713E-02 1,midg,midg; igrid,midg,midg 9.0667918E-02 9.1789067E-03 gauss-seidel spectral radius is 0.9992039 estimated iterations to convergence 280 setup time was (sec) 1.510000 now iterating at: 16:58:07 rms-change max change #iterations 8.956515 253.3854 at 10iterations 5.190476 123.5334 at 20iterations 2.978209 70.60055 at 30iterations 1.699289 40.40383 at 40iterations 0.9632462 25.06186 at 50iterations 0.5472288 13.22215 at 60iterations 0.3099886 8.369057 at 70iterations 0.1750051 3.380239 at 80iterations 9.8856367E-02 1.980673 at 90iterations 5.5719871E-02 1.155127 at 100iterations 3.1452715E-02 0.6665592 at 110iterations 1.7710414E-02 0.3522377 at 120iterations 9.9851117E-03 0.1878559 at 130iterations 5.6271525E-03 0.1203327 at 140iterations 3.1657771E-03 6.5086365E-02 at 150iterations 1.7865007E-03 3.8471222E-02 at 160iterations 1.0096532E-03 1.9630432E-02 at 170iterations 5.7200831E-04 1.1955738E-02 at 180iterations finished qdiffx linear iterations at : 16:58:17 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 5.7200831E-04 1.1955738E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 16:58:18 12.119u 0.192s 0:13.36 92.0% 0+0k 0+0io 0pf+0w