Sat Oct 8 11:34:01 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 Sat Oct 8 2011 at 11:34:01 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 = 3012 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: 0.6130532 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): 5.549000 63.61900 ymin,ymax (A): -8.035000 38.31300 zmin,zma (A): -19.38300 38.24000 x,y,z range (A): 58.07000 46.34800 57.62300 scale (grids/A): 0.6130532 object centre (A): 34.58400 15.13900 9.428501 number of atom coordinates read : 3012 total number of charged atoms : 2868 net assigned charge : -5.999961 assigned positive charge : 440.1039 centred at (gu) : 88.29394 90.57104 90.92933 assigned negative charge : -446.1050 centred at (gu) : 88.09934 90.68001 91.02331 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7573 nv = 96 ne = 84 npr = 63026 no. pairs analyzed = 63026 no. exposed pairs = 3679 no. arc points = 24593 no. surface atoms = 1255 nbur = 1757 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 4274 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2200000 number of dielectric boundary points 3617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2486 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9459 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7793245E-09 -1.1581589E-08 midg,1,midg; midg,igrid,midg 2.7402161E-09 -1.1770247E-08 1,midg,midg; igrid,midg,midg -2.3333996E-08 5.5894147E-09 gauss-seidel spectral radius is 0.9862550 estimated iterations to convergence 70 setup time was (sec) 0.4100000 now iterating at: 11:34:01 rms-change max change #iterations 0.1286686 19.48246 at 10iterations 1.1767733E-02 1.689064 at 20iterations 1.3030540E-03 0.2032509 at 30iterations 3.1416237E-04 4.9417496E-02 at 40iterations 1.1288146E-04 1.8247604E-02 at 50iterations finished qdiffx linear iterations at : 11:34:04 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.1288146E-04 1.8247604E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 11:34:05 3.573u 0.209s 0:04.37 86.2% 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 Sat Oct 8 2011 at 11:34:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 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: 1.839159 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): 5.549000 63.61900 ymin,ymax (A): -8.035000 38.31300 zmin,zma (A): -19.38300 38.24000 x,y,z range (A): 58.07000 46.34800 57.62300 scale (grids/A): 1.839159 object centre (A): 34.58400 15.13900 9.428501 number of atom coordinates read : 3012 total number of charged atoms : 2868 net assigned charge : -5.999961 assigned positive charge : 440.1039 centred at (gu) : 84.88090 91.71220 92.78708 assigned negative charge : -446.1050 centred at (gu) : 84.29753 92.03985 93.06971 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24593 grid for indexing accessible points = 1.400000 m= 29567 mr = 58904 m= 4387 mr = 21673 m= 222 mr = 2660 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1932 time to turn everything in is 0.4000000 number of dielectric boundary points 33336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22468 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) : 0.6130532 object centre at (A) : 34.58400 15.13900 9.428501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2380145E-02 -3.7139054E-02 midg,1,midg; midg,igrid,midg -6.4423620E-03 -2.5430724E-02 1,midg,midg; igrid,midg,midg -2.0757418E-02 4.5716871E-02 gauss-seidel spectral radius is 0.9985710 estimated iterations to convergence 210 setup time was (sec) 0.6400000 now iterating at: 11:34:06 rms-change max change #iterations 4.285426 178.1699 at 10iterations 1.969082 65.42863 at 20iterations 0.9073227 29.55468 at 30iterations 0.4191501 11.79751 at 40iterations 0.1931530 7.210852 at 50iterations 8.9101821E-02 2.858124 at 60iterations 4.1083943E-02 1.400965 at 70iterations 1.9035911E-02 0.6276093 at 80iterations 8.8070994E-03 0.3300972 at 90iterations 4.1190437E-03 0.1465583 at 100iterations 1.9705773E-03 5.9600830E-02 at 110iterations 9.7462168E-04 3.0244827E-02 at 120iterations finished qdiffx linear iterations at : 11:34:13 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 9.7462168E-04 3.0244827E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 11:34:14 8.201u 0.228s 0:08.77 96.0% 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 Sat Oct 8 2011 at 11:34:14 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 = 3012 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: 2.758739 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): 5.549000 63.61900 ymin,ymax (A): -8.035000 38.31300 zmin,zma (A): -19.38300 38.24000 x,y,z range (A): 58.07000 46.34800 57.62300 scale (grids/A): 2.758739 object centre (A): 34.58400 15.13900 9.428501 number of atom coordinates read : 3012 total number of charged atoms : 2868 net assigned charge : -5.999961 assigned positive charge : 440.1039 centred at (gu) : 82.32128 92.56812 94.18040 assigned negative charge : -446.1050 centred at (gu) : 81.44617 93.05957 94.60452 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 191365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24593 grid for indexing accessible points = 1.400000 m= 97114 mr = 143069 m= 33469 mr = 79508 m= 7716 mr = 26514 m= 1015 mr = 5711 m= 39 mr = 639 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 6344 time to turn everything in is 1.070000 number of dielectric boundary points 75266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 22938 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) : 1.839159 object centre at (A) : 34.58400 15.13900 9.428501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3866083 -0.3254896 midg,1,midg; midg,igrid,midg -9.7985499E-02 -0.2578783 1,midg,midg; igrid,midg,midg -0.3784520 0.5484108 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 1.350000 now iterating at: 11:34:16 rms-change max change #iterations 10.23013 299.1496 at 10iterations 6.009612 203.0074 at 20iterations 3.503440 86.24654 at 30iterations 2.031701 49.72205 at 40iterations 1.176751 24.96758 at 50iterations 0.6798642 14.15730 at 60iterations 0.3919939 8.308784 at 70iterations 0.2252238 4.746735 at 80iterations 0.1296724 2.340804 at 90iterations 7.4551187E-02 1.466013 at 100iterations 4.2810474E-02 0.7571049 at 110iterations 2.4669785E-02 0.4557838 at 120iterations 1.4203181E-02 0.2768936 at 130iterations 8.2493285E-03 0.1818771 at 140iterations 4.8302426E-03 9.1049194E-02 at 150iterations 2.8968120E-03 5.8097839E-02 at 160iterations 1.7972074E-03 3.5285950E-02 at 170iterations 1.1767431E-03 2.3166656E-02 at 180iterations finished qdiffx linear iterations at : 11:34:29 total time elapsed so far: 14.47000 # loops : 180 mean,max change (kT/e) : 1.1767431E-03 2.3166656E-02 energy calculations done at 14.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.59000 DelPhi exited at 11:34:29 14.596u 0.293s 0:15.37 96.8% 0+0k 0+0io 0pf+0w