Mon Oct 10 11:09:07 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 Mon Oct 10 2011 at 11:09:07 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 = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7456590 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): -22.23700 24.31100 ymin,ymax (A): -7.941000 36.11400 zmin,zma (A): -3.478000 44.26500 x,y,z range (A): 46.54800 44.05500 47.74300 scale (grids/A): 0.7456590 object centre (A): 1.037000 14.08650 20.39350 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 89.47784 90.43957 90.12009 assigned negative charge : -320.7320 centred at (gu) : 89.48509 90.49850 90.24845 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8117 nv = 96 ne = 84 npr = 43546 no. pairs analyzed = 43546 no. exposed pairs = 2671 no. arc points = 19011 no. surface atoms = 902 nbur = 1205 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 549 mr = 4522 m= 6 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.2700000 number of dielectric boundary points 4016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1503 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8408 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9369034E-08 -2.5838742E-07 midg,1,midg; midg,igrid,midg -3.4935134E-08 -1.8647138E-07 1,midg,midg; igrid,midg,midg -1.0542722E-07 -1.0256596E-07 gauss-seidel spectral radius is 0.9906274 estimated iterations to convergence 84 setup time was (sec) 0.5300000 now iterating at: 11:09:08 rms-change max change #iterations 0.2486037 33.16157 at 10iterations 3.4446120E-02 5.884984 at 20iterations 4.7022616E-03 0.6246986 at 30iterations 6.3583301E-04 7.8648090E-02 at 40iterations 8.8450099E-05 1.2645245E-02 at 50iterations finished qdiffx linear iterations at : 11:09:10 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 8.8450099E-05 1.2645245E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 11:09:11 3.601u 0.211s 0:04.22 90.2% 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 Mon Oct 10 2011 at 11:09:11 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 = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.236977 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): -22.23700 24.31100 ymin,ymax (A): -7.941000 36.11400 zmin,zma (A): -3.478000 44.26500 x,y,z range (A): 46.54800 44.05500 47.74300 scale (grids/A): 2.236977 object centre (A): 1.037000 14.08650 20.39350 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 88.43348 91.31874 90.36021 assigned negative charge : -320.7320 centred at (gu) : 88.45531 91.49556 90.74553 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19011 grid for indexing accessible points = 1.400000 m= 34448 mr = 58885 m= 7591 mr = 26359 m= 860 mr = 5354 m= 26 mr = 523 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1572 time to turn everything in is 0.6700000 number of dielectric boundary points 36808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15694 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) : 0.7456590 object centre at (A) : 1.037000 14.08650 20.39350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4347993E-03 -0.1146429 midg,1,midg; midg,igrid,midg -2.6903536E-02 -3.7842002E-02 1,midg,midg; igrid,midg,midg -4.6316017E-03 1.2139252E-03 gauss-seidel spectral radius is 0.9989397 estimated iterations to convergence 243 setup time was (sec) 0.9800000 now iterating at: 11:09:12 rms-change max change #iterations 5.123428 194.2155 at 10iterations 2.617712 83.54970 at 20iterations 1.336025 41.31993 at 30iterations 0.6868426 19.60253 at 40iterations 0.3506483 10.95206 at 50iterations 0.1800293 5.265848 at 60iterations 9.1979153E-02 2.774603 at 70iterations 4.7047045E-02 1.350578 at 80iterations 2.4169674E-02 0.7008057 at 90iterations 1.2349746E-02 0.3761272 at 100iterations 6.3274438E-03 0.1807404 at 110iterations 3.2373946E-03 9.6961975E-02 at 120iterations finished qdiffx linear iterations at : 11:09:19 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 3.2373946E-03 9.6961975E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 11:09:20 8.351u 0.244s 0:08.89 96.6% 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 Mon Oct 10 2011 at 11:09:20 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 = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.355465 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): -22.23700 24.31100 ymin,ymax (A): -7.941000 36.11400 zmin,zma (A): -3.478000 44.26500 x,y,z range (A): 46.54800 44.05500 47.74300 scale (grids/A): 3.355465 object centre (A): 1.037000 14.08650 20.39350 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 87.65018 91.97807 90.54034 assigned negative charge : -320.7320 centred at (gu) : 87.68304 92.24334 91.11821 start vw surface at 0.1400000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 195360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19011 grid for indexing accessible points = 1.400000 m= 105178 mr = 141330 m= 45620 mr = 87629 m= 14540 mr = 37965 m= 3583 mr = 11683 m= 479 mr = 2839 m= 22 mr = 344 m= 0 mr = 3 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 5428 time to turn everything in is 2.140000 number of dielectric boundary points 82989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 15752 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) : 2.236977 object centre at (A) : 1.037000 14.08650 20.39350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4649278E-04 -1.097310 midg,1,midg; midg,igrid,midg -0.2409462 -0.2031551 1,midg,midg; igrid,midg,midg -3.7798170E-02 -0.1535489 gauss-seidel spectral radius is 0.9993236 estimated iterations to convergence 303 setup time was (sec) 2.490000 now iterating at: 11:09:23 rms-change max change #iterations 11.06344 420.2283 at 10iterations 6.514590 115.0132 at 20iterations 3.851468 64.44530 at 30iterations 2.266590 37.65029 at 40iterations 1.335341 22.69913 at 50iterations 0.7879578 12.34598 at 60iterations 0.4647425 7.434485 at 70iterations 0.2729992 4.849200 at 80iterations 0.1606802 2.530212 at 90iterations 9.4518997E-02 1.506193 at 100iterations 5.5582814E-02 0.8662586 at 110iterations 3.2628480E-02 0.5355167 at 120iterations 1.9235838E-02 0.3467364 at 130iterations 1.1276960E-02 0.1749463 at 140iterations 6.6458709E-03 0.1074877 at 150iterations 3.9155311E-03 6.6518545E-02 at 160iterations 2.3024476E-03 3.6096811E-02 at 170iterations 1.3517929E-03 2.2660255E-02 at 180iterations finished qdiffx linear iterations at : 11:09:35 total time elapsed so far: 14.33000 # loops : 180 mean,max change (kT/e) : 1.3517929E-03 2.2660255E-02 energy calculations done at 14.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.52000 DelPhi exited at 11:09:35 14.523u 0.268s 0:15.06 98.1% 0+0k 0+0io 0pf+0w