Mon Oct 10 20:18:00 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 Mon Oct 10 2011 at 20:18:00 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 247 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6065356 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): -12.10000 45.15500 ymin,ymax (A): 30.06000 88.73400 zmin,zma (A): -13.13100 45.56300 x,y,z range (A): 57.25500 58.67400 58.69400 scale (grids/A): 0.6065356 object centre (A): 16.52750 59.39700 16.21600 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -2.471976 assigned positive charge : 455.8450 centred at (gu) : 89.13081 88.72687 90.90334 assigned negative charge : -458.3185 centred at (gu) : 89.13479 88.70663 91.01906 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7417 nv = 96 ne = 84 npr = 59738 no. pairs analyzed = 59738 no. exposed pairs = 4288 no. arc points = 30293 no. surface atoms = 1408 nbur = 1605 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3599 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3009 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9210 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8693142E-09 -9.0674748E-09 midg,1,midg; midg,igrid,midg -3.0446019E-09 -1.3870502E-10 1,midg,midg; igrid,midg,midg -1.2254906E-09 -1.1869519E-09 gauss-seidel spectral radius is 0.9859769 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 20:18:01 rms-change max change #iterations 0.1183552 18.44946 at 10iterations 1.0434824E-02 1.537567 at 20iterations 9.4873778E-04 0.1458683 at 30iterations 1.0994278E-04 1.8390417E-02 at 40iterations 1.9744713E-05 3.3140182E-03 at 50iterations finished qdiffx linear iterations at : 20:18:04 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 1.9744713E-05 3.3140182E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 20:18:05 3.178u 0.162s 0:04.20 79.2% 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 20:18:05 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 247 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.819607 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): -12.10000 45.15500 ymin,ymax (A): 30.06000 88.73400 zmin,zma (A): -13.13100 45.56300 x,y,z range (A): 57.25500 58.67400 58.69400 scale (grids/A): 1.819607 object centre (A): 16.52750 59.39700 16.21600 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -2.471976 assigned positive charge : 455.8450 centred at (gu) : 87.39160 86.17999 92.70885 assigned negative charge : -458.3185 centred at (gu) : 87.40385 86.11973 93.05672 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30293 grid for indexing accessible points = 1.400000 m= 27425 mr = 51335 m= 4140 mr = 18785 m= 198 mr = 2217 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 0.5800000 number of dielectric boundary points 38882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22482 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) : 0.6065356 object centre at (A) : 16.52750 59.39700 16.21600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3084642E-03 -5.3278264E-02 midg,1,midg; midg,igrid,midg 2.6660072E-02 -7.8850212E-03 1,midg,midg; igrid,midg,midg 9.7496808E-03 -1.7540891E-03 gauss-seidel spectral radius is 0.9985691 estimated iterations to convergence 210 setup time was (sec) 0.8500000 now iterating at: 20:18:06 rms-change max change #iterations 4.282208 185.7879 at 10iterations 1.947071 77.36978 at 20iterations 0.8939492 28.50398 at 30iterations 0.4119696 13.11560 at 40iterations 0.1879042 6.106668 at 50iterations 8.6310938E-02 2.770635 at 60iterations 3.9535634E-02 1.162659 at 70iterations 1.8166263E-02 0.5631657 at 80iterations 8.3601894E-03 0.2799177 at 90iterations 3.8409089E-03 0.1202030 at 100iterations 1.7735453E-03 5.6636810E-02 at 110iterations 8.1602536E-04 2.5947571E-02 at 120iterations finished qdiffx linear iterations at : 20:18:12 total time elapsed so far: 6.950000 # loops : 120 mean,max change (kT/e) : 8.1602536E-04 2.5947571E-02 energy calculations done at 6.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 20:18:12 7.123u 0.188s 0:07.63 95.6% 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 20:18:12 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 247 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.729410 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): -12.10000 45.15500 ymin,ymax (A): 30.06000 88.73400 zmin,zma (A): -13.13100 45.56300 x,y,z range (A): 57.25500 58.67400 58.69400 scale (grids/A): 2.729410 object centre (A): 16.52750 59.39700 16.21600 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -2.471976 assigned positive charge : 455.8450 centred at (gu) : 86.08724 84.26987 94.06298 assigned negative charge : -458.3185 centred at (gu) : 86.10569 84.17948 94.58510 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 183670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30293 grid for indexing accessible points = 1.400000 m= 87619 mr = 125698 m= 31546 mr = 68136 m= 7014 mr = 24005 m= 752 mr = 4737 m= 32 mr = 385 m= 0 mr = 2 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 297 time to turn everything in is 1.370000 number of dielectric boundary points 87670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 22974 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) : 1.819607 object centre at (A) : 16.52750 59.39700 16.21600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3704737E-02 -0.5718871 midg,1,midg; midg,igrid,midg 0.4785812 -4.1430268E-02 1,midg,midg; igrid,midg,midg 0.1600287 -5.4621086E-02 gauss-seidel spectral radius is 0.9992614 estimated iterations to convergence 290 setup time was (sec) 1.680000 now iterating at: 20:18:14 rms-change max change #iterations 10.35233 361.4532 at 10iterations 6.099583 140.6378 at 20iterations 3.550040 79.66180 at 30iterations 2.063750 43.08735 at 40iterations 1.199067 24.83955 at 50iterations 0.6926836 13.48734 at 60iterations 0.4005392 7.892025 at 70iterations 0.2307102 4.223118 at 80iterations 0.1331839 2.447989 at 90iterations 7.6550752E-02 1.470661 at 100iterations 4.4095926E-02 0.7748466 at 110iterations 2.5404049E-02 0.4536123 at 120iterations 1.4607565E-02 0.2555296 at 130iterations 8.3961925E-03 0.1450195 at 140iterations 4.8350552E-03 8.7783813E-02 at 150iterations 2.7825797E-03 4.9476624E-02 at 160iterations 1.6012555E-03 2.9736042E-02 at 170iterations 9.2489365E-04 1.7736435E-02 at 180iterations finished qdiffx linear iterations at : 20:18:24 total time elapsed so far: 11.41000 # loops : 180 mean,max change (kT/e) : 9.2489365E-04 1.7736435E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 20:18:25 11.586u 0.197s 0:12.39 94.9% 0+0k 0+0io 0pf+0w