Wed Dec 21 14:20:34 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 Wed Dec 21 2011 at 14:20:34 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1914 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: ASP 159 has a net charge of -0.2080 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6102369 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): -9.097000 49.24100 ymin,ymax (A): -18.72100 20.40800 zmin,zma (A): -7.874000 34.41100 x,y,z range (A): 58.33800 39.12900 42.28500 scale (grids/A): 0.6102369 object centre (A): 20.07200 0.8435001 13.26850 number of atom coordinates read : 1914 total number of charged atoms : 1782 net assigned charge : -2.067991 assigned positive charge : 279.2180 centred at (gu) : 90.15870 90.27006 89.46986 assigned negative charge : -281.2863 centred at (gu) : 90.14092 90.39087 89.39936 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4904 nv = 96 ne = 84 npr = 39078 no. pairs analyzed = 39078 no. exposed pairs = 2425 no. arc points = 16715 no. surface atoms = 822 nbur = 1092 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 213 mr = 2698 m= 0 mr = 17 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1646 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 5806 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2433315E-09 1.1706980E-09 midg,1,midg; midg,igrid,midg 2.9183382E-09 -5.9782574E-09 1,midg,midg; igrid,midg,midg -1.7792616E-09 -5.7597083E-10 gauss-seidel spectral radius is 0.9860401 estimated iterations to convergence 69 setup time was (sec) 0.3700000 now iterating at: 14:20:35 rms-change max change #iterations 0.1005229 18.83529 at 10iterations 8.7171979E-03 1.526005 at 20iterations 7.8011770E-04 0.1303997 at 30iterations 6.7819710E-05 1.1161804E-02 at 40iterations 5.8783235E-06 9.4795227E-04 at 50iterations finished qdiffx linear iterations at : 14:20:37 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.8783235E-06 9.4795227E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:20:38 3.397u 0.158s 0:03.84 92.1% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:20:38 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1914 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: ASP 159 has a net charge of -0.2080 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: 1.830711 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): -9.097000 49.24100 ymin,ymax (A): -18.72100 20.40800 zmin,zma (A): -7.874000 34.41100 x,y,z range (A): 58.33800 39.12900 42.28500 scale (grids/A): 1.830711 object centre (A): 20.07200 0.8435001 13.26850 number of atom coordinates read : 1914 total number of charged atoms : 1782 net assigned charge : -2.067991 assigned positive charge : 279.2180 centred at (gu) : 90.47630 90.81033 88.40955 assigned negative charge : -281.2863 centred at (gu) : 90.42313 91.17300 88.19843 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52894 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16715 grid for indexing accessible points = 1.400000 m= 18354 mr = 36537 m= 2378 mr = 13658 m= 97 mr = 1384 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.2700000 number of dielectric boundary points 22120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 13964 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) : 0.6102369 object centre at (A) : 20.07200 0.8435001 13.26850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7608985E-03 4.3741162E-03 midg,1,midg; midg,igrid,midg 3.0390860E-03 -8.6592995E-03 1,midg,midg; igrid,midg,midg 1.2995241E-02 2.1095889E-02 gauss-seidel spectral radius is 0.9984444 estimated iterations to convergence 201 setup time was (sec) 0.4900000 now iterating at: 14:20:39 rms-change max change #iterations 3.272396 159.0960 at 10iterations 1.452059 56.32930 at 20iterations 0.6470489 25.57059 at 30iterations 0.2886682 11.77339 at 40iterations 0.1279093 4.863754 at 50iterations 5.6813680E-02 2.229233 at 60iterations 2.5265438E-02 0.9593840 at 70iterations 1.1234193E-02 0.4353333 at 80iterations 5.0114607E-03 0.1914158 at 90iterations 2.2356515E-03 8.3034515E-02 at 100iterations 9.9292491E-04 3.5655975E-02 at 110iterations 4.4227604E-04 1.5472412E-02 at 120iterations finished qdiffx linear iterations at : 14:20:46 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 4.4227604E-04 1.5472412E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 14:20:47 8.202u 0.216s 0:08.97 93.7% 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 Wed Dec 21 2011 at 14:20:47 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1914 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: ASP 159 has a net charge of -0.2080 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: 2.746066 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): -9.097000 49.24100 ymin,ymax (A): -18.72100 20.40800 zmin,zma (A): -7.874000 34.41100 x,y,z range (A): 58.33800 39.12900 42.28500 scale (grids/A): 2.746066 object centre (A): 20.07200 0.8435001 13.26850 number of atom coordinates read : 1914 total number of charged atoms : 1782 net assigned charge : -2.067991 assigned positive charge : 279.2180 centred at (gu) : 90.71440 91.21550 87.61443 assigned negative charge : -281.2863 centred at (gu) : 90.63465 91.75948 87.29793 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 122480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16715 grid for indexing accessible points = 1.400000 m= 60865 mr = 88538 m= 20156 mr = 50083 m= 3993 mr = 16227 m= 414 mr = 2954 m= 15 mr = 240 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.6700000 number of dielectric boundary points 49881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 14256 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) : 1.830711 object centre at (A) : 20.07200 0.8435001 13.26850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0659410E-02 3.9433502E-02 midg,1,midg; midg,igrid,midg 2.3178538E-02 -7.8862697E-02 1,midg,midg; igrid,midg,midg 0.1774900 0.3477869 gauss-seidel spectral radius is 0.9991876 estimated iterations to convergence 277 setup time was (sec) 0.9000000 now iterating at: 14:20:48 rms-change max change #iterations 7.826930 267.7319 at 10iterations 4.445203 116.2350 at 20iterations 2.501388 56.26563 at 30iterations 1.401203 29.13490 at 40iterations 0.7855837 16.87789 at 50iterations 0.4380781 9.216164 at 60iterations 0.2454640 6.145631 at 70iterations 0.1371219 2.769466 at 80iterations 7.6511398E-02 1.720443 at 90iterations 4.2784806E-02 0.9133034 at 100iterations 2.3916656E-02 0.5542033 at 110iterations 1.3341869E-02 0.2884998 at 120iterations 7.4428115E-03 0.1779938 at 130iterations 4.1568242E-03 8.4433556E-02 at 140iterations 2.3255374E-03 4.8059464E-02 at 150iterations 1.2934394E-03 2.6396751E-02 at 160iterations 7.2452659E-04 1.6058147E-02 at 170iterations 4.0507739E-04 8.7934136E-03 at 180iterations finished qdiffx linear iterations at : 14:20:59 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 4.0507739E-04 8.7934136E-03 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.94000 DelPhi exited at 14:21:00 11.941u 0.229s 0:12.72 95.5% 0+0k 0+0io 0pf+0w