Wed Dec 21 14:21:00 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+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 Wed Dec 21 2011 at 14:21:00 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: 279 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: ASL 30 has a net charge of -0.1000 !!! 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 : -2.167992 assigned positive charge : 283.9180 centred at (gu) : 90.16365 90.26103 89.51334 assigned negative charge : -286.0863 centred at (gu) : 90.14714 90.38056 89.44813 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 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 = 5.9999995E-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 = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1400000 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 0.2200000 number of grid points assigned charge 5806 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0995549E-09 9.9440067E-10 midg,1,midg; midg,igrid,midg 2.8921103E-09 -6.0610095E-09 1,midg,midg; igrid,midg,midg -1.8028760E-09 -6.7759470E-10 gauss-seidel spectral radius is 0.9860401 estimated iterations to convergence 69 setup time was (sec) 0.3400000 now iterating at: 14:21:00 rms-change max change #iterations 0.1058293 21.90653 at 10iterations 9.1030002E-03 1.557529 at 20iterations 8.1150589E-04 0.1365647 at 30iterations 7.0910166E-05 1.1634827E-02 at 40iterations 6.1602655E-06 9.9563599E-04 at 50iterations finished qdiffx linear iterations at : 14:21:03 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.1602655E-06 9.9563599E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:21:05 3.403u 0.244s 0:05.25 69.3% 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 14:21:05 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: 279 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: ASL 30 has a net charge of -0.1000 !!! 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 : -2.167992 assigned positive charge : 283.9180 centred at (gu) : 90.49119 90.78328 88.53996 assigned negative charge : -286.0863 centred at (gu) : 90.44173 91.14201 88.34470 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 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 = 0.1100000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.2800000 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 0.3400000 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 -9.2005879E-03 4.2074407E-03 midg,1,midg; midg,igrid,midg 3.2855889E-03 -8.8006891E-03 1,midg,midg; igrid,midg,midg 1.2648733E-02 2.0745778E-02 gauss-seidel spectral radius is 0.9984444 estimated iterations to convergence 201 setup time was (sec) 0.5000000 now iterating at: 14:21:06 rms-change max change #iterations 3.355520 159.0960 at 10iterations 1.486970 58.83977 at 20iterations 0.6631014 25.40801 at 30iterations 0.2956294 11.61072 at 40iterations 0.1309788 4.875700 at 50iterations 5.8152188E-02 2.317867 at 60iterations 2.5861403E-02 0.9809122 at 70iterations 1.1503015E-02 0.4379740 at 80iterations 5.1336470E-03 0.1964817 at 90iterations 2.2892077E-03 8.5307121E-02 at 100iterations 1.0172009E-03 3.5613537E-02 at 110iterations 4.5269777E-04 1.7242432E-02 at 120iterations finished qdiffx linear iterations at : 14:21:14 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 4.5269777E-04 1.7242432E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 14:21:15 8.170u 0.241s 0:09.54 88.1% 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 Wed Dec 21 2011 at 14:21:15 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: 279 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: ASL 30 has a net charge of -0.1000 !!! 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 : -2.167992 assigned positive charge : 283.9180 centred at (gu) : 90.73672 91.17488 87.81007 assigned negative charge : -286.0863 centred at (gu) : 90.66254 91.71301 87.51733 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 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 = 0.3700000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.6800000 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 0.7700000 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 -8.4035836E-02 4.0958624E-02 midg,1,midg; midg,igrid,midg 2.7577071E-02 -8.0496974E-02 1,midg,midg; igrid,midg,midg 0.1735461 0.3435629 gauss-seidel spectral radius is 0.9991876 estimated iterations to convergence 277 setup time was (sec) 0.9100000 now iterating at: 14:21:16 rms-change max change #iterations 7.995894 267.7574 at 10iterations 4.539521 117.6202 at 20iterations 2.554992 59.53748 at 30iterations 1.430373 29.81111 at 40iterations 0.8018631 17.14773 at 50iterations 0.4472212 9.667313 at 60iterations 0.2504182 6.406678 at 70iterations 0.1398489 2.979202 at 80iterations 7.8014843E-02 1.798034 at 90iterations 4.3674015E-02 0.9183760 at 100iterations 2.4388250E-02 0.5548210 at 110iterations 1.3604150E-02 0.2985764 at 120iterations 7.5936550E-03 0.1869555 at 130iterations 4.2417203E-03 8.6939812E-02 at 140iterations 2.3711426E-03 5.0103664E-02 at 150iterations 1.3197723E-03 2.6801586E-02 at 160iterations 7.3902548E-04 1.6556025E-02 at 170iterations 4.1317387E-04 8.8195801E-03 at 180iterations finished qdiffx linear iterations at : 14:21:27 total time elapsed so far: 11.83000 # loops : 180 mean,max change (kT/e) : 4.1317387E-04 8.8195801E-03 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 14:21:36 11.980u 0.216s 0:20.73 58.8% 0+0k 0+0io 0pf+0w