Tue Oct 11 06:09:31 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 Tue Oct 11 2011 at 06:09:31 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 = 2065 !!! WARNING: SEP 190 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: 0.7155204 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): 3.508000 46.14600 ymin,ymax (A): 0.6060001 41.42500 zmin,zma (A): -2.677000 47.07700 x,y,z range (A): 42.63800 40.81900 49.75400 scale (grids/A): 0.7155204 object centre (A): 24.82700 21.01550 22.20000 number of atom coordinates read : 2065 total number of charged atoms : 1935 net assigned charge : 7.025010 assigned positive charge : 313.9371 centred at (gu) : 90.45654 90.24847 90.58326 assigned negative charge : -306.9122 centred at (gu) : 90.65302 90.24237 90.62046 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7323 nv = 96 ne = 84 npr = 41296 no. pairs analyzed = 41296 no. exposed pairs = 2526 no. arc points = 17084 no. surface atoms = 861 nbur = 1204 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4295 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1526 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7833 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4201375E-08 5.6391052E-08 midg,1,midg; midg,igrid,midg 6.5777030E-08 7.9577433E-08 1,midg,midg; igrid,midg,midg 1.6889108E-07 -4.8609291E-08 gauss-seidel spectral radius is 0.9898148 estimated iterations to convergence 81 setup time was (sec) 0.5000000 now iterating at: 06:09:31 rms-change max change #iterations 0.2121612 28.33116 at 10iterations 2.6909914E-02 3.821881 at 20iterations 3.8734220E-03 0.5140676 at 30iterations 7.6219288E-04 9.9727631E-02 at 40iterations 2.2902536E-04 2.9918671E-02 at 50iterations finished qdiffx linear iterations at : 06:09:34 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 2.2902536E-04 2.9918671E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 06:09:34 3.297u 0.165s 0:03.83 90.0% 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 06:09:35 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 = 2065 !!! WARNING: SEP 190 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: 2.146561 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): 3.508000 46.14600 ymin,ymax (A): 0.6060001 41.42500 zmin,zma (A): -2.677000 47.07700 x,y,z range (A): 42.63800 40.81900 49.75400 scale (grids/A): 2.146561 object centre (A): 24.82700 21.01550 22.20000 number of atom coordinates read : 2065 total number of charged atoms : 1935 net assigned charge : 7.025010 assigned positive charge : 313.9371 centred at (gu) : 91.36977 90.74532 91.74978 assigned negative charge : -306.9122 centred at (gu) : 91.95912 90.72702 91.86142 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17084 grid for indexing accessible points = 1.400000 m= 31801 mr = 55228 m= 6399 mr = 24404 m= 554 mr = 4371 m= 7 mr = 242 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15384 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) : 0.7155204 object centre at (A) : 24.82700 21.01550 22.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3534536E-02 6.9504522E-02 midg,1,midg; midg,igrid,midg 7.1780737E-03 3.0435784E-02 1,midg,midg; igrid,midg,midg 4.6456650E-02 -5.0493879E-03 gauss-seidel spectral radius is 0.9988523 estimated iterations to convergence 234 setup time was (sec) 0.8700000 now iterating at: 06:09:36 rms-change max change #iterations 4.715678 161.8884 at 10iterations 2.345476 81.80766 at 20iterations 1.175844 38.54218 at 30iterations 0.5862596 16.36825 at 40iterations 0.2939986 9.741455 at 50iterations 0.1473144 4.628093 at 60iterations 7.3827162E-02 2.213892 at 70iterations 3.7044756E-02 1.140976 at 80iterations 1.8701466E-02 0.6067524 at 90iterations 9.5863808E-03 0.3044205 at 100iterations 4.9331263E-03 0.1499786 at 110iterations 2.6393959E-03 8.0436707E-02 at 120iterations finished qdiffx linear iterations at : 06:09:42 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 2.6393959E-03 8.0436707E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 06:09:43 7.480u 0.170s 0:08.14 93.9% 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 06:09:43 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 = 2065 !!! WARNING: SEP 190 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: 3.219842 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): 3.508000 46.14600 ymin,ymax (A): 0.6060001 41.42500 zmin,zma (A): -2.677000 47.07700 x,y,z range (A): 42.63800 40.81900 49.75400 scale (grids/A): 3.219842 object centre (A): 24.82700 21.01550 22.20000 number of atom coordinates read : 2065 total number of charged atoms : 1935 net assigned charge : 7.025010 assigned positive charge : 313.9371 centred at (gu) : 92.05476 91.11800 92.62475 assigned negative charge : -306.9122 centred at (gu) : 92.93865 91.09056 92.79207 start vw surface at 0.1500000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 177457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17084 grid for indexing accessible points = 1.400000 m= 98336 mr = 132535 m= 40950 mr = 82512 m= 12037 mr = 34041 m= 2321 mr = 9394 m= 167 mr = 1587 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.900000 number of dielectric boundary points 71117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 15480 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) : 2.146561 object centre at (A) : 24.82700 21.01550 22.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3290229 0.7246820 midg,1,midg; midg,igrid,midg 5.8213957E-03 0.2311006 1,midg,midg; igrid,midg,midg 0.3397692 4.8756894E-02 gauss-seidel spectral radius is 0.9992994 estimated iterations to convergence 298 setup time was (sec) 2.200000 now iterating at: 06:09:45 rms-change max change #iterations 10.35375 367.2749 at 10iterations 6.142544 122.3921 at 20iterations 3.632750 80.08879 at 30iterations 2.148668 44.05907 at 40iterations 1.265315 25.62041 at 50iterations 0.7444921 13.59247 at 60iterations 0.4383248 7.855239 at 70iterations 0.2577691 4.447453 at 80iterations 0.1513150 2.859364 at 90iterations 8.9092366E-02 1.479711 at 100iterations 5.2414678E-02 0.9666758 at 110iterations 3.1024450E-02 0.5486565 at 120iterations 1.8514859E-02 0.3340902 at 130iterations 1.1285414E-02 0.2068863 at 140iterations 7.0987293E-03 0.1383133 at 150iterations 4.6584643E-03 8.8447571E-02 at 160iterations 3.2527321E-03 6.5105438E-02 at 170iterations 2.4151476E-03 4.3708801E-02 at 180iterations finished qdiffx linear iterations at : 06:09:55 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 2.4151476E-03 4.3708801E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 06:09:56 12.494u 0.172s 0:12.98 97.5% 0+0k 0+0io 0pf+0w