Tue Oct 11 08:29:51 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 Tue Oct 11 2011 at 08:29:51 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4144 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 223 has a net charge of -0.4750 !!! WARNING: HIR 294 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5317640 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): -30.81100 30.15000 ymin,ymax (A): -24.27300 37.05900 zmin,zma (A): -38.70300 28.24400 x,y,z range (A): 60.96100 61.33200 66.94700 scale (grids/A): 0.5317640 object centre (A): -0.3304996 6.393002 -5.229500 number of atom coordinates read : 4144 total number of charged atoms : 3993 net assigned charge : -1.529964 assigned positive charge : 625.5989 centred at (gu) : 87.56869 90.02475 90.47532 assigned negative charge : -627.1324 centred at (gu) : 87.56516 90.14565 90.50375 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7656 nv = 96 ne = 84 npr = 82280 no. pairs analyzed = 82280 no. exposed pairs = 5477 no. arc points = 38362 no. surface atoms = 1822 nbur = 2322 mkacc time = 0.2000000 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 = 1.624000 m= 306 mr = 3805 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3980 ## 575 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10152 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9184340E-11 -2.3180784E-10 midg,1,midg; midg,igrid,midg 5.8608596E-10 -7.1781558E-10 1,midg,midg; igrid,midg,midg -1.3050468E-10 -1.8342831E-11 gauss-seidel spectral radius is 0.9818750 estimated iterations to convergence 61 setup time was (sec) 0.7100000 now iterating at: 08:29:51 rms-change max change #iterations 7.8858629E-02 12.61149 at 10iterations 5.0529134E-03 0.6696701 at 20iterations 4.3139758E-04 7.2565079E-02 at 30iterations 9.2820468E-05 1.4341831E-02 at 40iterations 2.7313818E-05 4.3058395E-03 at 50iterations finished qdiffx linear iterations at : 08:29:54 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.7313818E-05 4.3058395E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 08:29:55 3.496u 0.149s 0:03.94 92.1% 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 Tue Oct 11 2011 at 08:29:55 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4144 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 223 has a net charge of -0.4750 !!! WARNING: HIR 294 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.595292 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): -30.81100 30.15000 ymin,ymax (A): -24.27300 37.05900 zmin,zma (A): -38.70300 28.24400 x,y,z range (A): 60.96100 61.33200 66.94700 scale (grids/A): 1.595292 object centre (A): -0.3304996 6.393002 -5.229500 number of atom coordinates read : 4144 total number of charged atoms : 3993 net assigned charge : -1.529964 assigned positive charge : 625.5989 centred at (gu) : 82.70444 90.07265 91.42440 assigned negative charge : -627.1324 centred at (gu) : 82.69495 90.43643 91.51066 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 84643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38362 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25452 mr = 55863 m= 2285 mr = 16896 m= 53 mr = 947 m= 0 mr = 1 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.6400000 number of dielectric boundary points 38726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 526 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 30406 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) : 0.5317640 object centre at (A) : -0.3304996 6.393002 -5.229500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8161396E-03 -7.6104430E-03 midg,1,midg; midg,igrid,midg 6.5364037E-03 -1.3500837E-02 1,midg,midg; igrid,midg,midg 1.6175088E-02 8.0064116E-03 gauss-seidel spectral radius is 0.9982261 estimated iterations to convergence 189 setup time was (sec) 0.9100000 now iterating at: 08:29:56 rms-change max change #iterations 3.833018 150.1428 at 10iterations 1.605656 59.83661 at 20iterations 0.6766648 22.39534 at 30iterations 0.2851692 9.658943 at 40iterations 0.1194414 3.772778 at 50iterations 5.0450362E-02 1.522237 at 60iterations 2.1186752E-02 0.6947289 at 70iterations 8.9595132E-03 0.2929368 at 80iterations 3.7856023E-03 0.1248226 at 90iterations 1.5965850E-03 5.5686951E-02 at 100iterations 6.7996385E-04 2.1717072E-02 at 110iterations 2.9240263E-04 9.8824501E-03 at 120iterations finished qdiffx linear iterations at : 08:30:02 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 2.9240263E-04 9.8824501E-03 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 08:30:03 7.572u 0.184s 0:08.04 96.3% 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 Tue Oct 11 2011 at 08:30:03 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4144 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: SEP 81 has a net charge of -0.4750 !!! WARNING: SEP 223 has a net charge of -0.4750 !!! WARNING: HIR 294 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.392938 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): -30.81100 30.15000 ymin,ymax (A): -24.27300 37.05900 zmin,zma (A): -38.70300 28.24400 x,y,z range (A): 60.96100 61.33200 66.94700 scale (grids/A): 2.392938 object centre (A): -0.3304996 6.393002 -5.229500 number of atom coordinates read : 4144 total number of charged atoms : 3993 net assigned charge : -1.529964 assigned positive charge : 625.5989 centred at (gu) : 79.05638 90.10853 92.13624 assigned negative charge : -627.1324 centred at (gu) : 79.04231 90.65459 92.26586 start vw surface at 0.2000000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 196383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38362 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 89346 mr = 137152 m= 23954 mr = 69310 m= 3332 mr = 17419 m= 194 mr = 1899 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 356 time to turn everything in is 1.510000 number of dielectric boundary points 87382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 31879 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) : 1.595292 object centre at (A) : -0.3304996 6.393002 -5.229500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2819215 -0.1939470 midg,1,midg; midg,igrid,midg 7.6842181E-02 -0.1810950 1,midg,midg; igrid,midg,midg 0.2228830 6.6256560E-02 gauss-seidel spectral radius is 0.9991895 estimated iterations to convergence 277 setup time was (sec) 1.810000 now iterating at: 08:30:05 rms-change max change #iterations 10.22637 307.3185 at 10iterations 5.941365 138.8452 at 20iterations 3.429195 75.99796 at 30iterations 1.960346 41.34508 at 40iterations 1.116013 25.53030 at 50iterations 0.6332906 14.30743 at 60iterations 0.3588502 6.836110 at 70iterations 0.2022289 3.891250 at 80iterations 0.1142870 2.223246 at 90iterations 6.4355358E-02 1.224719 at 100iterations 3.6278572E-02 0.6975222 at 110iterations 2.0354871E-02 0.3774481 at 120iterations 1.1447605E-02 0.2285471 at 130iterations 6.4215981E-03 0.1233213 at 140iterations 3.6175668E-03 7.1813583E-02 at 150iterations 2.0323452E-03 4.0591240E-02 at 160iterations 1.1476977E-03 2.0278931E-02 at 170iterations 6.4728153E-04 1.1741638E-02 at 180iterations finished qdiffx linear iterations at : 08:30:15 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 6.4728153E-04 1.1741638E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 08:30:15 12.237u 0.187s 0:12.73 97.4% 0+0k 0+0io 0pf+0w