Sun Oct 9 11:31:35 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 Sun Oct 9 2011 at 11:31:35 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: CME 112 has a net charge of -0.3480 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 454 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 !!! WARNING: CME 4 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of 0.1000 !!! WARNING: CME 8 has a net charge of 0.1000 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: 0.5865102 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): -20.48000 40.21800 ymin,ymax (A): -25.55800 23.99700 zmin,zma (A): -27.88700 27.39400 x,y,z range (A): 60.69800 49.55500 55.28100 scale (grids/A): 0.5865102 object centre (A): 9.869001 -0.7805004 -0.2465000 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : 1.508031 assigned positive charge : 430.2270 centred at (gu) : 89.59126 90.89087 91.03755 assigned negative charge : -428.7207 centred at (gu) : 89.58482 90.82308 90.98220 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6982 nv = 96 ne = 84 npr = 58445 no. pairs analyzed = 58445 no. exposed pairs = 4094 no. arc points = 28450 no. surface atoms = 1346 nbur = 1597 mkacc time = 0.1200000 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 = 1.484000 m= 378 mr = 3554 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2818 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4590718E-10 2.3241851E-09 midg,1,midg; midg,igrid,midg -1.1445506E-09 2.6424891E-09 1,midg,midg; igrid,midg,midg 2.2830425E-10 4.9848742E-10 gauss-seidel spectral radius is 0.9850031 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 11:31:36 rms-change max change #iterations 0.1003003 17.80278 at 10iterations 8.0894595E-03 1.315739 at 20iterations 8.7100937E-04 0.1366119 at 30iterations 1.7493208E-04 2.5603294E-02 at 40iterations 4.9267972E-05 7.4558258E-03 at 50iterations finished qdiffx linear iterations at : 11:31:39 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 4.9267972E-05 7.4558258E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:31:39 3.388u 0.176s 0:03.83 92.6% 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 Sun Oct 9 2011 at 11:31:39 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: CME 112 has a net charge of -0.3480 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 454 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 !!! WARNING: CME 4 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of 0.1000 !!! WARNING: CME 8 has a net charge of 0.1000 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: 1.759531 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): -20.48000 40.21800 ymin,ymax (A): -25.55800 23.99700 zmin,zma (A): -27.88700 27.39400 x,y,z range (A): 60.69800 49.55500 55.28100 scale (grids/A): 1.759531 object centre (A): 9.869001 -0.7805004 -0.2465000 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : 1.508031 assigned positive charge : 430.2270 centred at (gu) : 88.77290 92.67154 93.11169 assigned negative charge : -428.7207 centred at (gu) : 88.75431 92.46918 92.94650 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75557 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 grid for indexing accessible points = 1.400000 m= 26081 mr = 50574 m= 3732 mr = 17824 m= 193 mr = 1923 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 35221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21835 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) : 0.5865102 object centre at (A) : 9.869001 -0.7805004 -0.2465000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2048630E-02 9.9799512E-03 midg,1,midg; midg,igrid,midg 5.5747190E-03 1.8480783E-02 1,midg,midg; igrid,midg,midg 1.2888195E-02 -1.0481367E-02 gauss-seidel spectral radius is 0.9984636 estimated iterations to convergence 202 setup time was (sec) 0.8500000 now iterating at: 11:31:40 rms-change max change #iterations 3.819284 160.2135 at 10iterations 1.697674 60.51905 at 20iterations 0.7608330 27.35759 at 30iterations 0.3386369 11.58733 at 40iterations 0.1516023 5.121794 at 50iterations 6.7739889E-02 2.377892 at 60iterations 3.0364238E-02 0.9506044 at 70iterations 1.3627548E-02 0.4456406 at 80iterations 6.1895484E-03 0.2069130 at 90iterations 2.8216881E-03 8.9871883E-02 at 100iterations 1.3175275E-03 4.6909332E-02 at 110iterations 6.3558947E-04 2.1942139E-02 at 120iterations finished qdiffx linear iterations at : 11:31:47 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 6.3558947E-04 2.1942139E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 11:31:48 8.116u 0.211s 0:08.65 96.1% 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 11:31:48 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2943 !!! WARNING: CME 112 has a net charge of -0.3480 !!! WARNING: CME 217 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 454 has a net charge of -0.3480 !!! WARNING: CME 2 has a net charge of 0.1000 !!! WARNING: CME 4 has a net charge of 0.1000 !!! WARNING: CME 6 has a net charge of 0.1000 !!! WARNING: CME 8 has a net charge of 0.1000 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: 2.639296 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): -20.48000 40.21800 ymin,ymax (A): -25.55800 23.99700 zmin,zma (A): -27.88700 27.39400 x,y,z range (A): 60.69800 49.55500 55.28100 scale (grids/A): 2.639296 object centre (A): 9.869001 -0.7805004 -0.2465000 number of atom coordinates read : 2943 total number of charged atoms : 2803 net assigned charge : 1.508031 assigned positive charge : 430.2270 centred at (gu) : 88.15907 94.00726 94.66737 assigned negative charge : -428.7207 centred at (gu) : 88.13150 93.70375 94.41962 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 174791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 grid for indexing accessible points = 1.400000 m= 85009 mr = 123802 m= 29525 mr = 66444 m= 6451 mr = 22283 m= 692 mr = 4209 m= 27 mr = 298 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 79461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 22414 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) : 1.759531 object centre at (A) : 9.869001 -0.7805004 -0.2465000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1729542 0.1309274 midg,1,midg; midg,igrid,midg 0.1290823 0.1767979 1,midg,midg; igrid,midg,midg 0.2749769 -0.1299857 gauss-seidel spectral radius is 0.9992262 estimated iterations to convergence 284 setup time was (sec) 1.620000 now iterating at: 11:31:50 rms-change max change #iterations 9.541351 294.3587 at 10iterations 5.584311 146.2602 at 20iterations 3.235082 78.63995 at 30iterations 1.868997 41.56084 at 40iterations 1.073892 22.07711 at 50iterations 0.6167578 14.02569 at 60iterations 0.3532482 6.856642 at 70iterations 0.2016998 4.008547 at 80iterations 0.1152766 2.214508 at 90iterations 6.5567032E-02 1.304723 at 100iterations 3.7351422E-02 0.7432785 at 110iterations 2.1251660E-02 0.4280548 at 120iterations 1.2125553E-02 0.2559824 at 130iterations 6.9194655E-03 0.1265106 at 140iterations 3.9525391E-03 7.8735352E-02 at 150iterations 2.2746352E-03 4.6735764E-02 at 160iterations 1.3154155E-03 2.5646210E-02 at 170iterations 7.7560096E-04 2.1977425E-02 at 180iterations finished qdiffx linear iterations at : 11:32:00 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 7.7560096E-04 2.1977425E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 11:32:01 12.574u 0.264s 0:13.10 97.9% 0+0k 0+0io 0pf+0w