Tue Oct 11 04:22:36 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 Tue Oct 11 2011 at 04:22:36 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6722689 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): -15.28100 32.82100 ymin,ymax (A): 6.767000 55.08100 zmin,zma (A): 25.63800 78.59300 x,y,z range (A): 48.10200 48.31400 52.95500 scale (grids/A): 0.6722689 object centre (A): 8.770000 30.92400 52.11550 number of atom coordinates read : 2752 total number of charged atoms : 2600 net assigned charge : 3.162015 assigned positive charge : 414.7977 centred at (gu) : 90.23342 90.60455 88.69896 assigned negative charge : -411.6363 centred at (gu) : 90.55244 90.43770 88.64091 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8357 nv = 96 ne = 84 npr = 57029 no. pairs analyzed = 57029 no. exposed pairs = 3297 no. arc points = 23151 no. surface atoms = 1108 nbur = 1644 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 504 mr = 4811 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 58 time to turn everything in is 0.2100000 number of dielectric boundary points 3980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2222 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9747 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0299846E-09 2.1463824E-08 midg,1,midg; midg,igrid,midg -3.2487129E-08 6.6015083E-08 1,midg,midg; igrid,midg,midg 9.4792796E-08 -8.6761069E-08 gauss-seidel spectral radius is 0.9885398 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 04:22:37 rms-change max change #iterations 0.1830752 21.61059 at 10iterations 2.0486746E-02 2.557863 at 20iterations 2.2912573E-03 0.3111115 at 30iterations 2.7011908E-04 3.2363892E-02 at 40iterations 3.6186302E-05 4.9114227E-03 at 50iterations finished qdiffx linear iterations at : 04:22:40 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.6186302E-05 4.9114227E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 04:22:40 3.393u 0.174s 0:04.00 89.0% 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 Tue Oct 11 2011 at 04:22:40 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.016807 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): -15.28100 32.82100 ymin,ymax (A): 6.767000 55.08100 zmin,zma (A): 25.63800 78.59300 x,y,z range (A): 48.10200 48.31400 52.95500 scale (grids/A): 2.016807 object centre (A): 8.770000 30.92400 52.11550 number of atom coordinates read : 2752 total number of charged atoms : 2600 net assigned charge : 3.162015 assigned positive charge : 414.7977 centred at (gu) : 90.69965 91.81281 86.09654 assigned negative charge : -411.6363 centred at (gu) : 91.65705 91.31292 85.92251 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 89182 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23151 grid for indexing accessible points = 1.400000 m= 34806 mr = 63420 m= 6246 mr = 26440 m= 462 mr = 4097 m= 11 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1577 time to turn everything in is 0.4400000 number of dielectric boundary points 36521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20544 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) : 0.6722689 object centre at (A) : 8.770000 30.92400 52.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5951477E-02 1.4490868E-02 midg,1,midg; midg,igrid,midg -1.8669762E-02 4.7548380E-02 1,midg,midg; igrid,midg,midg 8.9732721E-02 -2.9857181E-02 gauss-seidel spectral radius is 0.9987872 estimated iterations to convergence 227 setup time was (sec) 0.6600000 now iterating at: 04:22:41 rms-change max change #iterations 4.872175 197.7579 at 10iterations 2.393889 72.32350 at 20iterations 1.168809 39.06140 at 30iterations 0.5746747 20.23077 at 40iterations 0.2816591 8.618847 at 50iterations 0.1379233 4.083817 at 60iterations 6.7696474E-02 1.849453 at 70iterations 3.3211119E-02 0.9066648 at 80iterations 1.6238486E-02 0.4513283 at 90iterations 7.9742689E-03 0.2186625 at 100iterations 3.9030209E-03 0.1108704 at 110iterations 1.9165620E-03 5.4784775E-02 at 120iterations finished qdiffx linear iterations at : 04:22:48 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.9165620E-03 5.4784775E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 04:22:49 7.822u 0.190s 0:08.55 93.6% 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 Tue Oct 11 2011 at 04:22:49 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 3.025210 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): -15.28100 32.82100 ymin,ymax (A): 6.767000 55.08100 zmin,zma (A): 25.63800 78.59300 x,y,z range (A): 48.10200 48.31400 52.95500 scale (grids/A): 3.025210 object centre (A): 8.770000 30.92400 52.11550 number of atom coordinates read : 2752 total number of charged atoms : 2600 net assigned charge : 3.162015 assigned positive charge : 414.7977 centred at (gu) : 91.04945 92.71908 84.14473 assigned negative charge : -411.6363 centred at (gu) : 92.48547 91.96924 83.88375 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 206114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23151 grid for indexing accessible points = 1.400000 m= 109477 mr = 153077 m= 43343 mr = 91025 m= 11533 mr = 35728 m= 1933 mr = 8967 m= 196 mr = 1295 m= 7 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 5205 time to turn everything in is 1.150000 number of dielectric boundary points 82375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 20789 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) : 2.016807 object centre at (A) : 8.770000 30.92400 52.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5097176E-02 7.4316017E-02 midg,1,midg; midg,igrid,midg -0.1950284 0.5314690 1,midg,midg; igrid,midg,midg 0.7176851 -0.1614471 gauss-seidel spectral radius is 0.9992934 estimated iterations to convergence 297 setup time was (sec) 1.390000 now iterating at: 04:22:51 rms-change max change #iterations 11.14290 470.4064 at 10iterations 6.576892 156.2166 at 20iterations 3.872389 88.61642 at 30iterations 2.280231 38.96467 at 40iterations 1.336919 22.49700 at 50iterations 0.7845061 14.20225 at 60iterations 0.4594872 9.262033 at 70iterations 0.2694697 4.724419 at 80iterations 0.1575107 2.650913 at 90iterations 9.2030503E-02 1.742683 at 100iterations 5.3738758E-02 0.9366646 at 110iterations 3.1400383E-02 0.5127697 at 120iterations 1.8312519E-02 0.3054657 at 130iterations 1.0704089E-02 0.1859970 at 140iterations 6.2644072E-03 0.1000900 at 150iterations 3.6714822E-03 6.4956665E-02 at 160iterations 2.1618679E-03 3.5312653E-02 at 170iterations 1.2760985E-03 2.2603989E-02 at 180iterations finished qdiffx linear iterations at : 04:23:02 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.2760985E-03 2.2603989E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 04:23:03 12.873u 0.199s 0:13.73 95.1% 0+0k 0+0io 0pf+0w