Sun Oct 9 07:30:54 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 Sun Oct 9 2011 at 07:30:54 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 = 2513 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: 0.5757630 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): -4.485000 50.22000 ymin,ymax (A): 6.518000 57.21400 zmin,zma (A): 53.24000 115.0710 x,y,z range (A): 54.70500 50.69600 61.83100 scale (grids/A): 0.5757630 object centre (A): 22.86750 31.86600 84.15550 number of atom coordinates read : 2513 total number of charged atoms : 2368 net assigned charge : -11.49998 assigned positive charge : 375.8619 centred at (gu) : 89.95092 90.36129 87.93126 assigned negative charge : -387.3623 centred at (gu) : 89.83608 90.70984 87.71906 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5451 nv = 96 ne = 84 npr = 50303 no. pairs analyzed = 50303 no. exposed pairs = 3464 no. arc points = 24699 no. surface atoms = 1173 nbur = 1340 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 = 1.512000 m= 230 mr = 2577 m= 0 mr = 13 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7009 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2327843E-09 8.2056689E-10 midg,1,midg; midg,igrid,midg 3.2010841E-09 -8.7685255E-09 1,midg,midg; igrid,midg,midg -4.0045252E-09 -1.5851945E-10 gauss-seidel spectral radius is 0.9844010 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 07:30:55 rms-change max change #iterations 8.4372155E-02 15.01050 at 10iterations 6.3187885E-03 1.208068 at 20iterations 4.7719639E-04 8.4923029E-02 at 30iterations 3.6908426E-05 6.8244934E-03 at 40iterations 2.9079270E-06 4.5394897E-04 at 50iterations finished qdiffx linear iterations at : 07:30:57 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.9079270E-06 4.5394897E-04 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 07:30:58 3.090u 0.136s 0:03.50 92.0% 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 Sun Oct 9 2011 at 07:30:58 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 = 2513 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: 1.727289 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): -4.485000 50.22000 ymin,ymax (A): 6.518000 57.21400 zmin,zma (A): 53.24000 115.0710 x,y,z range (A): 54.70500 50.69600 61.83100 scale (grids/A): 1.727289 object centre (A): 22.86750 31.86600 84.15550 number of atom coordinates read : 2513 total number of charged atoms : 2368 net assigned charge : -11.49998 assigned positive charge : 375.8619 centred at (gu) : 89.85207 91.08347 83.79324 assigned negative charge : -387.3623 centred at (gu) : 89.50788 92.12919 83.15674 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24699 grid for indexing accessible points = 1.400000 m= 18593 mr = 37112 m= 2090 mr = 12654 m= 39 mr = 1103 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 417 time to turn everything in is 0.4500000 number of dielectric boundary points 28651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 18325 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) : 0.5757630 object centre at (A) : 22.86750 31.86600 84.15550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0268670E-02 1.0768371E-02 midg,1,midg; midg,igrid,midg 5.6109380E-04 -3.6211360E-02 1,midg,midg; igrid,midg,midg -2.6057029E-02 -1.6322615E-02 gauss-seidel spectral radius is 0.9983324 estimated iterations to convergence 194 setup time was (sec) 0.7500000 now iterating at: 07:30:58 rms-change max change #iterations 3.423492 198.9946 at 10iterations 1.470693 56.70513 at 20iterations 0.6346371 26.43016 at 30iterations 0.2741020 10.31928 at 40iterations 0.1182177 4.333624 at 50iterations 5.0847620E-02 1.911602 at 60iterations 2.1951046E-02 0.8063535 at 70iterations 9.5032426E-03 0.3568125 at 80iterations 4.1000862E-03 0.1451678 at 90iterations 1.7768098E-03 6.2981606E-02 at 100iterations 7.6539879E-04 2.8650284E-02 at 110iterations 3.3002463E-04 1.1844635E-02 at 120iterations finished qdiffx linear iterations at : 07:31:05 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 3.3002463E-04 1.1844635E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 07:31:06 7.542u 0.224s 0:08.04 96.5% 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 Sun Oct 9 2011 at 07:31:06 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 = 2513 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: 2.590934 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): -4.485000 50.22000 ymin,ymax (A): 6.518000 57.21400 zmin,zma (A): 53.24000 115.0710 x,y,z range (A): 54.70500 50.69600 61.83100 scale (grids/A): 2.590934 object centre (A): 22.86750 31.86600 84.15550 number of atom coordinates read : 2513 total number of charged atoms : 2368 net assigned charge : -11.49998 assigned positive charge : 375.8619 centred at (gu) : 89.77816 91.62506 80.68974 assigned negative charge : -387.3623 centred at (gu) : 89.26186 93.19373 79.73510 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 136038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24699 grid for indexing accessible points = 1.400000 m= 62518 mr = 91003 m= 19401 mr = 48628 m= 3310 mr = 14822 m= 193 mr = 2185 m= 3 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 1381 time to turn everything in is 1.060000 number of dielectric boundary points 64722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 18933 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) : 1.727289 object centre at (A) : 22.86750 31.86600 84.15550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4714021 -5.1895726E-02 midg,1,midg; midg,igrid,midg 3.2042187E-02 -0.4248632 1,midg,midg; igrid,midg,midg -0.1949283 -0.2530214 gauss-seidel spectral radius is 0.9991811 estimated iterations to convergence 276 setup time was (sec) 1.370000 now iterating at: 07:31:07 rms-change max change #iterations 8.729033 340.2616 at 10iterations 4.997294 121.1256 at 20iterations 2.840209 76.07968 at 30iterations 1.602972 38.92615 at 40iterations 0.9051699 24.35590 at 50iterations 0.5085651 11.32782 at 60iterations 0.2853763 6.925800 at 70iterations 0.1601832 3.443665 at 80iterations 8.9805037E-02 1.985618 at 90iterations 5.0169643E-02 1.061783 at 100iterations 2.8053071E-02 0.5784416 at 110iterations 1.5697425E-02 0.3518257 at 120iterations 8.7459553E-03 0.1788275 at 130iterations 4.8842761E-03 0.1026397 at 140iterations 2.7259469E-03 5.6244373E-02 at 150iterations 1.5198523E-03 3.2974243E-02 at 160iterations 8.4860966E-04 2.1955490E-02 at 170iterations 4.7318841E-04 1.0330200E-02 at 180iterations finished qdiffx linear iterations at : 07:31:18 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 4.7318841E-04 1.0330200E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 07:31:18 12.307u 0.258s 0:12.82 97.8% 0+0k 0+0io 0pf+0w