Sun Oct 9 22:49:44 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 Sun Oct 9 2011 at 22:49:45 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4251 !!! WARNING: SEP 108 has a net charge of -0.4750 !!! WARNING: SEP 477 has a net charge of -0.4750 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: 0.5268376 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): 35.62800 99.66100 ymin,ymax (A): -20.64600 46.92700 zmin,zma (A): 18.61300 71.39600 x,y,z range (A): 64.03300 67.57300 52.78300 scale (grids/A): 0.5268376 object centre (A): 67.64450 13.14050 45.00450 number of atom coordinates read : 4251 total number of charged atoms : 4090 net assigned charge : 2.050013 assigned positive charge : 644.3856 centred at (gu) : 90.23318 91.21670 89.44836 assigned negative charge : -642.3394 centred at (gu) : 90.25594 91.29319 89.51785 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7668 nv = 96 ne = 84 npr = 83534 no. pairs analyzed = 83534 no. exposed pairs = 5518 no. arc points = 39123 no. surface atoms = 1858 nbur = 2393 mkacc time = 0.1400000 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= 287 mr = 3934 m= 1 mr = 5 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 0.2900000 number of dielectric boundary points 4017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3847 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 10187 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3409881E-10 -2.2344318E-10 midg,1,midg; midg,igrid,midg 2.9835384E-10 -4.0119386E-10 1,midg,midg; igrid,midg,midg 1.5591001E-10 -4.5097294E-11 gauss-seidel spectral radius is 0.9815402 estimated iterations to convergence 61 setup time was (sec) 0.4900000 now iterating at: 22:49:45 rms-change max change #iterations 7.1945697E-02 11.73716 at 10iterations 4.4740043E-03 0.6694260 at 20iterations 2.9441435E-04 4.5024872E-02 at 30iterations 4.3160951E-05 1.0422647E-02 at 40iterations 1.4082038E-05 3.5587549E-03 at 50iterations finished qdiffx linear iterations at : 22:49:48 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.4082038E-05 3.5587549E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 22:49:49 3.522u 0.170s 0:04.02 91.7% 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 Sun Oct 9 2011 at 22:49:49 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4251 !!! WARNING: SEP 108 has a net charge of -0.4750 !!! WARNING: SEP 477 has a net charge of -0.4750 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: 1.580513 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): 35.62800 99.66100 ymin,ymax (A): -20.64600 46.92700 zmin,zma (A): 18.61300 71.39600 x,y,z range (A): 64.03300 67.57300 52.78300 scale (grids/A): 1.580513 object centre (A): 67.64450 13.14050 45.00450 number of atom coordinates read : 4251 total number of charged atoms : 4090 net assigned charge : 2.050013 assigned positive charge : 644.3856 centred at (gu) : 90.69778 93.64869 88.34370 assigned negative charge : -642.3394 centred at (gu) : 90.76764 93.87882 88.55316 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86237 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39123 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25768 mr = 58389 m= 2403 mr = 17552 m= 50 mr = 1157 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 37358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 523 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 31089 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) : 0.5268376 object centre at (A) : 67.64450 13.14050 45.00450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0044330E-03 -1.0151829E-02 midg,1,midg; midg,igrid,midg 2.8883735E-02 -1.9073931E-03 1,midg,midg; igrid,midg,midg 1.2522511E-02 1.5484650E-02 gauss-seidel spectral radius is 0.9981962 estimated iterations to convergence 187 setup time was (sec) 0.6300000 now iterating at: 22:49:49 rms-change max change #iterations 3.788521 150.8830 at 10iterations 1.577810 50.02325 at 20iterations 0.6593860 22.24440 at 30iterations 0.2758762 9.125734 at 40iterations 0.1152485 3.667412 at 50iterations 4.8097461E-02 1.567303 at 60iterations 2.0119082E-02 0.6655655 at 70iterations 8.4260246E-03 0.2557297 at 80iterations 3.5339457E-03 0.1072111 at 90iterations 1.4842792E-03 4.5761108E-02 at 100iterations 6.3119922E-04 2.1048069E-02 at 110iterations 2.7198260E-04 8.3503723E-03 at 120iterations finished qdiffx linear iterations at : 22:49:57 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.7198260E-04 8.3503723E-03 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 22:49:57 7.916u 0.210s 0:08.39 96.7% 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 Sun Oct 9 2011 at 22:49:57 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4251 !!! WARNING: SEP 108 has a net charge of -0.4750 !!! WARNING: SEP 477 has a net charge of -0.4750 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: 2.370770 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): 35.62800 99.66100 ymin,ymax (A): -20.64600 46.92700 zmin,zma (A): 18.61300 71.39600 x,y,z range (A): 64.03300 67.57300 52.78300 scale (grids/A): 2.370770 object centre (A): 67.64450 13.14050 45.00450 number of atom coordinates read : 4251 total number of charged atoms : 4090 net assigned charge : 2.050013 assigned positive charge : 644.3856 centred at (gu) : 91.04647 95.47267 87.51519 assigned negative charge : -642.3394 centred at (gu) : 91.15140 95.81802 87.82950 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 200580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39123 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 91004 mr = 143393 m= 24340 mr = 71541 m= 3458 mr = 17964 m= 188 mr = 2255 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 84334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 32651 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) : 1.580513 object centre at (A) : 67.64450 13.14050 45.00450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9424089E-02 -0.1500254 midg,1,midg; midg,igrid,midg 0.3987539 -0.3134057 1,midg,midg; igrid,midg,midg 0.3004611 0.3815455 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.270000 now iterating at: 22:49:58 rms-change max change #iterations 10.22949 258.4143 at 10iterations 5.950571 147.6512 at 20iterations 3.422409 75.07986 at 30iterations 1.957485 40.00768 at 40iterations 1.115292 28.39460 at 50iterations 0.6311429 12.92634 at 60iterations 0.3569145 8.307077 at 70iterations 0.2009143 3.643211 at 80iterations 0.1130415 2.009628 at 90iterations 6.3478902E-02 1.179527 at 100iterations 3.5625849E-02 0.7466011 at 110iterations 1.9960567E-02 0.3875775 at 120iterations 1.1188216E-02 0.1995010 at 130iterations 6.2624975E-03 0.1144733 at 140iterations 3.5092337E-03 6.6839218E-02 at 150iterations 1.9687023E-03 3.6415100E-02 at 160iterations 1.1115487E-03 1.9304276E-02 at 170iterations 6.2918762E-04 1.1050165E-02 at 180iterations finished qdiffx linear iterations at : 22:50:10 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 6.2918762E-04 1.1050165E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 22:50:10 12.966u 0.205s 0:13.45 97.8% 0+0k 0+0io 0pf+0w