Mon Oct 10 17:03:15 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 17:03:15 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4637 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5226609 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): -25.12700 38.69500 ymin,ymax (A): -18.04600 48.34100 zmin,zma (A): 7.104001 75.21700 x,y,z range (A): 63.82200 66.38700 68.11300 scale (grids/A): 0.5226609 object centre (A): 6.784000 15.14750 41.16050 number of atom coordinates read : 4637 total number of charged atoms : 4397 net assigned charge : 7.800027 assigned positive charge : 702.1115 centred at (gu) : 91.81033 88.28643 87.76594 assigned negative charge : -694.3156 centred at (gu) : 91.91442 88.39367 87.63218 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8125 nv = 96 ne = 84 npr = 92212 no. pairs analyzed = 92212 no. exposed pairs = 6100 no. arc points = 41864 no. surface atoms = 2035 nbur = 2602 mkacc time = 0.2700000 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= 321 mr = 4144 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4067 ## 547 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 10681 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6011496E-10 4.1781034E-10 midg,1,midg; midg,igrid,midg 9.9116726E-10 -1.5610817E-10 1,midg,midg; igrid,midg,midg 3.9106951E-10 -3.8433459E-10 gauss-seidel spectral radius is 0.9812706 estimated iterations to convergence 60 setup time was (sec) 0.8300000 now iterating at: 17:03:16 rms-change max change #iterations 7.5699694E-02 14.23641 at 10iterations 4.9752723E-03 0.7267685 at 20iterations 8.8087632E-04 0.1256800 at 30iterations 3.4392084E-04 4.9912453E-02 at 40iterations 1.4008675E-04 2.0327568E-02 at 50iterations finished qdiffx linear iterations at : 17:03:23 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 1.4008675E-04 2.0327568E-02 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 17:03:24 4.685u 0.308s 0:08.82 56.4% 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 17:03:24 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4637 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.567983 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): -25.12700 38.69500 ymin,ymax (A): -18.04600 48.34100 zmin,zma (A): 7.104001 75.21700 x,y,z range (A): 63.82200 66.38700 68.11300 scale (grids/A): 1.567983 object centre (A): 6.784000 15.14750 41.16050 number of atom coordinates read : 4637 total number of charged atoms : 4397 net assigned charge : 7.800027 assigned positive charge : 702.1115 centred at (gu) : 95.42920 84.85821 83.29628 assigned negative charge : -694.3156 centred at (gu) : 95.74321 85.18037 82.89627 start vw surface at 0.2100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 91953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41864 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27078 mr = 62533 m= 2477 mr = 17956 m= 52 mr = 1067 m= 0 mr = 4 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 833 time to turn everything in is 0.8500000 number of dielectric boundary points 40000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 451 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 33274 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) : 0.5226609 object centre at (A) : 6.784000 15.14750 41.16050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9424345E-03 2.3202566E-02 midg,1,midg; midg,igrid,midg 8.2151489E-03 -9.8253461E-03 1,midg,midg; igrid,midg,midg 1.1245116E-02 3.1795364E-03 gauss-seidel spectral radius is 0.9981958 estimated iterations to convergence 187 setup time was (sec) 1.190000 now iterating at: 17:03:25 rms-change max change #iterations 3.956220 155.7278 at 10iterations 1.651651 51.31718 at 20iterations 0.6881618 24.92843 at 30iterations 0.2884150 8.727669 at 40iterations 0.1203671 3.607866 at 50iterations 5.0527871E-02 1.608215 at 60iterations 2.1191666E-02 0.6462708 at 70iterations 8.9953402E-03 0.2761211 at 80iterations 3.8595253E-03 0.1230354 at 90iterations 1.7504124E-03 5.9224486E-02 at 100iterations 8.8250358E-04 3.1541824E-02 at 110iterations 5.1513530E-04 2.0792007E-02 at 120iterations finished qdiffx linear iterations at : 17:03:35 total time elapsed so far: 11.02000 # loops : 120 mean,max change (kT/e) : 5.1513530E-04 2.0792007E-02 energy calculations done at 11.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 17:03:36 11.216u 0.581s 0:12.32 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 17:03:36 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4637 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.351974 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): -25.12700 38.69500 ymin,ymax (A): -18.04600 48.34100 zmin,zma (A): 7.104001 75.21700 x,y,z range (A): 63.82200 66.38700 68.11300 scale (grids/A): 2.351974 object centre (A): 6.784000 15.14750 41.16050 number of atom coordinates read : 4637 total number of charged atoms : 4397 net assigned charge : 7.800027 assigned positive charge : 702.1115 centred at (gu) : 98.14348 82.28703 79.94405 assigned negative charge : -694.3156 centred at (gu) : 98.61475 82.77045 79.34425 start vw surface at 0.2200000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 213924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41864 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 96524 mr = 153855 m= 24987 mr = 74989 m= 3641 mr = 17830 m= 217 mr = 2245 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 2702 time to turn everything in is 2.100000 number of dielectric boundary points 90292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 35098 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) : 1.567983 object centre at (A) : 6.784000 15.14750 41.16050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6452662 0.5083365 midg,1,midg; midg,igrid,midg 8.3632492E-02 -0.1756888 1,midg,midg; igrid,midg,midg 0.1764128 9.8032907E-02 gauss-seidel spectral radius is 0.9991841 estimated iterations to convergence 276 setup time was (sec) 2.540000 now iterating at: 17:03:40 rms-change max change #iterations 10.50600 258.2283 at 10iterations 6.050158 134.1369 at 20iterations 3.471053 73.93674 at 30iterations 1.978145 43.46288 at 40iterations 1.121106 21.46480 at 50iterations 0.6353661 12.59888 at 60iterations 0.3582229 6.827403 at 70iterations 0.2019070 4.035195 at 80iterations 0.1135536 2.484315 at 90iterations 6.3988097E-02 1.342417 at 100iterations 3.5929445E-02 0.6986294 at 110iterations 2.0216184E-02 0.4051933 at 120iterations 1.1323309E-02 0.2131596 at 130iterations 6.3761934E-03 0.1299973 at 140iterations 3.5922951E-03 6.8328857E-02 at 150iterations 2.0396160E-03 3.9056778E-02 at 160iterations 1.1725230E-03 2.2950411E-02 at 170iterations 6.9303124E-04 1.4469147E-02 at 180iterations finished qdiffx linear iterations at : 17:03:58 total time elapsed so far: 21.43000 # loops : 180 mean,max change (kT/e) : 6.9303124E-04 1.4469147E-02 energy calculations done at 21.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.63000 DelPhi exited at 17:04:00 21.633u 0.532s 0:23.72 93.4% 0+0k 0+0io 0pf+0w