Sat Oct 15 14:09:38 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 Sat Oct 15 2011 at 14:09:38 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 = 4787 !!! WARNING: HEM 819 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5123555 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): -16.08900 37.39300 ymin,ymax (A): -30.49200 35.40200 zmin,zma (A): -4.044000 65.43900 x,y,z range (A): 53.48200 65.89400 69.48300 scale (grids/A): 0.5123555 object centre (A): 10.65200 2.455000 30.69750 number of atom coordinates read : 4787 total number of charged atoms : 4536 net assigned charge : 6.800031 assigned positive charge : 717.0223 centred at (gu) : 89.56220 90.40266 88.26377 assigned negative charge : -710.2268 centred at (gu) : 89.43537 90.42332 88.24226 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8000 nv = 96 ne = 84 npr = 96540 no. pairs analyzed = 96540 no. exposed pairs = 6082 no. arc points = 42430 no. surface atoms = 2038 nbur = 2749 mkacc time = 0.1600000 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 = 1.652000 m= 307 mr = 4151 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4028 ## 599 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2563025E-11 1.0669889E-10 midg,1,midg; midg,igrid,midg 1.4808461E-10 5.5041114E-11 1,midg,midg; igrid,midg,midg -2.8154104E-10 4.0328194E-10 gauss-seidel spectral radius is 0.9805208 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 14:09:38 rms-change max change #iterations 7.0360713E-02 10.76740 at 10iterations 4.3635471E-03 0.5784073 at 20iterations 6.8504282E-04 9.4977498E-02 at 30iterations 2.6649208E-04 3.8138390E-02 at 40iterations 1.1169424E-04 1.6191721E-02 at 50iterations finished qdiffx linear iterations at : 14:09:43 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 1.1169424E-04 1.6191721E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 14:09:44 3.633u 0.197s 0:06.38 59.8% 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 Sat Oct 15 2011 at 14:09:44 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 = 4787 !!! WARNING: HEM 819 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.537067 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): -16.08900 37.39300 ymin,ymax (A): -30.49200 35.40200 zmin,zma (A): -4.044000 65.43900 x,y,z range (A): 53.48200 65.89400 69.48300 scale (grids/A): 1.537067 object centre (A): 10.65200 2.455000 30.69750 number of atom coordinates read : 4787 total number of charged atoms : 4536 net assigned charge : 6.800031 assigned positive charge : 717.0223 centred at (gu) : 88.68539 91.20668 84.78967 assigned negative charge : -710.2268 centred at (gu) : 88.30572 91.26983 84.72669 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 90812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42430 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25798 mr = 62272 m= 2253 mr = 16930 m= 56 mr = 940 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.4500000 number of dielectric boundary points 38771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 581 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 34118 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) : 0.5123555 object centre at (A) : 10.65200 2.455000 30.69750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9555877E-03 1.7067308E-02 midg,1,midg; midg,igrid,midg 1.9994318E-03 -9.0225767E-03 1,midg,midg; igrid,midg,midg -1.2232179E-03 1.2256630E-02 gauss-seidel spectral radius is 0.9981323 estimated iterations to convergence 184 setup time was (sec) 0.6800000 now iterating at: 14:09:45 rms-change max change #iterations 3.836059 183.8555 at 10iterations 1.573357 53.84333 at 20iterations 0.6508033 21.62196 at 30iterations 0.2689720 8.208857 at 40iterations 0.1109039 3.667803 at 50iterations 4.5869771E-02 1.565781 at 60iterations 1.8857360E-02 0.6250687 at 70iterations 7.8490498E-03 0.2702150 at 80iterations 3.2328451E-03 0.1007729 at 90iterations 1.3444405E-03 4.1828156E-02 at 100iterations 5.7032483E-04 1.7780304E-02 at 110iterations 2.5408168E-04 8.5010529E-03 at 120iterations finished qdiffx linear iterations at : 14:09:54 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 2.5408168E-04 8.5010529E-03 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 14:09:55 8.521u 0.223s 0:11.13 78.5% 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 Sat Oct 15 2011 at 14:09:55 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 = 4787 !!! WARNING: HEM 819 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.305600 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): -16.08900 37.39300 ymin,ymax (A): -30.49200 35.40200 zmin,zma (A): -4.044000 65.43900 x,y,z range (A): 53.48200 65.89400 69.48300 scale (grids/A): 2.305600 object centre (A): 10.65200 2.455000 30.69750 number of atom coordinates read : 4787 total number of charged atoms : 4536 net assigned charge : 6.800031 assigned positive charge : 717.0223 centred at (gu) : 88.02779 91.80948 82.18406 assigned negative charge : -710.2268 centred at (gu) : 87.45844 91.90460 82.09002 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 211522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42430 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93369 mr = 152993 m= 23210 mr = 72570 m= 3340 mr = 16322 m= 211 mr = 2025 m= 1 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 156 time to turn everything in is 1.130000 number of dielectric boundary points 87653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 36190 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) : 1.537067 object centre at (A) : 10.65200 2.455000 30.69750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1330321 0.4379934 midg,1,midg; midg,igrid,midg -2.7470766E-02 -0.2588516 1,midg,midg; igrid,midg,midg -1.4010061E-02 0.1880564 gauss-seidel spectral radius is 0.9991708 estimated iterations to convergence 274 setup time was (sec) 1.390000 now iterating at: 14:09:57 rms-change max change #iterations 10.29591 264.3405 at 10iterations 5.919323 168.1849 at 20iterations 3.379066 77.84216 at 30iterations 1.914423 44.31589 at 40iterations 1.083336 22.76685 at 50iterations 0.6122641 13.65532 at 60iterations 0.3435203 7.741021 at 70iterations 0.1923918 3.883062 at 80iterations 0.1077617 2.366756 at 90iterations 6.0300667E-02 1.136865 at 100iterations 3.3664133E-02 0.6425610 at 110iterations 1.8789658E-02 0.3770809 at 120iterations 1.0479139E-02 0.2122459 at 130iterations 5.8550015E-03 0.1207676 at 140iterations 3.2715772E-03 6.0222626E-02 at 150iterations 1.8290834E-03 3.4897327E-02 at 160iterations 1.0313470E-03 2.1115303E-02 at 170iterations 5.8643846E-04 1.1769772E-02 at 180iterations finished qdiffx linear iterations at : 14:10:14 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 5.8643846E-04 1.1769772E-02 energy calculations done at 14.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.50000 DelPhi exited at 14:10:15 14.500u 0.278s 0:19.65 75.1% 0+0k 0+0io 0pf+0w