Sun Oct 9 04:26:38 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 04:26:38 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 = 3738 !!! WARNING: HEM 500 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5581687 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): -24.90200 38.87800 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 63.78000 53.66500 58.91900 scale (grids/A): 0.5581687 object centre (A): 6.988001 28.28450 -4.026500 number of atom coordinates read : 3738 total number of charged atoms : 3548 net assigned charge : 2.900021 assigned positive charge : 543.7795 centred at (gu) : 89.17434 89.37691 91.59165 assigned negative charge : -540.8812 centred at (gu) : 89.13342 89.39658 91.66840 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7583 nv = 96 ne = 84 npr = 77638 no. pairs analyzed = 77638 no. exposed pairs = 4703 no. arc points = 33275 no. surface atoms = 1573 nbur = 2165 mkacc time = 0.1300000 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 = 1.540000 m= 326 mr = 4015 m= 0 mr = 22 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3259 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6000645E-10 -9.9968800E-10 midg,1,midg; midg,igrid,midg 6.4440436E-10 5.3030871E-11 1,midg,midg; igrid,midg,midg -2.6056129E-10 6.7136235E-10 gauss-seidel spectral radius is 0.9835066 estimated iterations to convergence 64 setup time was (sec) 0.4600000 now iterating at: 04:26:39 rms-change max change #iterations 9.3892217E-02 15.09287 at 10iterations 6.9773770E-03 0.9594879 at 20iterations 6.3713233E-04 0.1101732 at 30iterations 1.1211596E-04 2.6815414E-02 at 40iterations 2.7711410E-05 6.8855286E-03 at 50iterations finished qdiffx linear iterations at : 04:26:42 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.7711410E-05 6.8855286E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 04:26:43 3.573u 0.181s 0:04.03 93.0% 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 Sun Oct 9 2011 at 04:26:43 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3738 !!! WARNING: HEM 500 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.674506 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): -24.90200 38.87800 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 63.78000 53.66500 58.91900 scale (grids/A): 1.674506 object centre (A): 6.988001 28.28450 -4.026500 number of atom coordinates read : 3738 total number of charged atoms : 3548 net assigned charge : 2.900021 assigned positive charge : 543.7795 centred at (gu) : 87.52194 88.12955 94.77408 assigned negative charge : -540.8812 centred at (gu) : 87.39953 88.18908 95.00464 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 83896 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33275 grid for indexing accessible points = 1.400000 m= 27268 mr = 57524 m= 3182 mr = 19097 m= 98 mr = 1707 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 0.4100000 number of dielectric boundary points 36104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 318 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 27398 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) : 0.5581687 object centre at (A) : 6.988001 28.28450 -4.026500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4412279E-03 -2.0125788E-02 midg,1,midg; midg,igrid,midg 2.0630876E-02 1.1487804E-02 1,midg,midg; igrid,midg,midg 9.8034358E-03 -6.8145068E-03 gauss-seidel spectral radius is 0.9983627 estimated iterations to convergence 196 setup time was (sec) 0.6400000 now iterating at: 04:26:43 rms-change max change #iterations 3.960666 159.0348 at 10iterations 1.716681 56.06896 at 20iterations 0.7479132 28.68536 at 30iterations 0.3255231 11.06155 at 40iterations 0.1422895 4.678963 at 50iterations 6.1987288E-02 2.097453 at 60iterations 2.6965877E-02 0.7852020 at 70iterations 1.1831313E-02 0.3613062 at 80iterations 5.1707993E-03 0.1639735 at 90iterations 2.2665130E-03 7.1585178E-02 at 100iterations 9.9369418E-04 3.2165527E-02 at 110iterations 4.4214871E-04 1.3532639E-02 at 120iterations finished qdiffx linear iterations at : 04:26:51 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 4.4214871E-04 1.3532639E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 04:26:51 8.156u 0.224s 0:08.73 95.8% 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 04:26:51 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 = 3738 !!! WARNING: HEM 500 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.511759 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): -24.90200 38.87800 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 63.78000 53.66500 58.91900 scale (grids/A): 2.511759 object centre (A): 6.988001 28.28450 -4.026500 number of atom coordinates read : 3738 total number of charged atoms : 3548 net assigned charge : 2.900021 assigned positive charge : 543.7795 centred at (gu) : 86.28267 87.19401 97.16083 assigned negative charge : -540.8812 centred at (gu) : 86.09919 87.28336 97.50677 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 194869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33275 grid for indexing accessible points = 1.400000 m= 91994 mr = 140580 m= 28744 mr = 73147 m= 5213 mr = 22245 m= 434 mr = 3622 m= 8 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 2187 time to turn everything in is 1.030000 number of dielectric boundary points 81433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 28358 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) : 1.674506 object centre at (A) : 6.988001 28.28450 -4.026500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5402725E-02 -0.2056619 midg,1,midg; midg,igrid,midg 0.3096207 0.1953555 1,midg,midg; igrid,midg,midg 0.4647190 -3.3402499E-02 gauss-seidel spectral radius is 0.9992132 estimated iterations to convergence 281 setup time was (sec) 1.270000 now iterating at: 04:26:53 rms-change max change #iterations 9.993666 304.6199 at 10iterations 5.733034 126.5598 at 20iterations 3.285889 64.66187 at 30iterations 1.873874 38.17916 at 40iterations 1.069666 21.27209 at 50iterations 0.6085246 13.70580 at 60iterations 0.3448317 6.453638 at 70iterations 0.1956220 3.808783 at 80iterations 0.1109282 1.978254 at 90iterations 6.2590696E-02 1.129602 at 100iterations 3.5404027E-02 0.6388607 at 110iterations 2.0039845E-02 0.3989828 at 120iterations 1.1327548E-02 0.2038708 at 130iterations 6.4024874E-03 0.1191387 at 140iterations 3.6280288E-03 6.4579010E-02 at 150iterations 2.0481662E-03 3.8703918E-02 at 160iterations 1.1641318E-03 2.1839142E-02 at 170iterations 6.5997813E-04 1.2737274E-02 at 180iterations finished qdiffx linear iterations at : 04:27:05 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 6.5997813E-04 1.2737274E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.55000 DelPhi exited at 04:27:05 13.548u 0.242s 0:14.06 98.0% 0+0k 0+0io 0pf+0w