Sat Oct 15 11:53:03 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 Sat Oct 15 2011 at 11:53:03 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6383360 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): -13.14000 39.70900 ymin,ymax (A): -30.48200 25.28800 zmin,zma (A): 3.054000 45.27000 x,y,z range (A): 52.84900 55.77000 42.21600 scale (grids/A): 0.6383360 object centre (A): 13.28450 -2.597000 24.16200 number of atom coordinates read : 2204 total number of charged atoms : 2070 net assigned charge : 8.000025 assigned positive charge : 319.2597 centred at (gu) : 90.91044 91.01557 88.76537 assigned negative charge : -311.2602 centred at (gu) : 90.84800 91.05051 88.88124 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6235 nv = 96 ne = 84 npr = 43729 no. pairs analyzed = 43729 no. exposed pairs = 2990 no. arc points = 21527 no. surface atoms = 995 nbur = 1209 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3146 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2047 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7259 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7492787E-08 4.6764026E-10 midg,1,midg; midg,igrid,midg 1.1340505E-08 9.5641086E-09 1,midg,midg; igrid,midg,midg 4.4492738E-09 1.9933982E-08 gauss-seidel spectral radius is 0.9872630 estimated iterations to convergence 72 setup time was (sec) 0.3500000 now iterating at: 11:53:03 rms-change max change #iterations 0.1345301 21.16510 at 10iterations 1.2859081E-02 1.963558 at 20iterations 1.2424293E-03 0.1831665 at 30iterations 1.2312697E-04 1.9703865E-02 at 40iterations 1.2143717E-05 1.8596649E-03 at 50iterations finished qdiffx linear iterations at : 11:53:06 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.2143717E-05 1.8596649E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 11:53:07 3.340u 0.183s 0:03.79 92.8% 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 11:53:07 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.915008 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): -13.14000 39.70900 ymin,ymax (A): -30.48200 25.28800 zmin,zma (A): 3.054000 45.27000 x,y,z range (A): 52.84900 55.77000 42.21600 scale (grids/A): 1.915008 object centre (A): 13.28450 -2.597000 24.16200 number of atom coordinates read : 2204 total number of charged atoms : 2070 net assigned charge : 8.000025 assigned positive charge : 319.2597 centred at (gu) : 92.73129 93.04663 86.29603 assigned negative charge : -311.2602 centred at (gu) : 92.54417 93.15164 86.64414 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 66456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21527 grid for indexing accessible points = 1.400000 m= 23616 mr = 43644 m= 3676 mr = 16651 m= 234 mr = 2087 m= 5 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 335 time to turn everything in is 0.3200000 number of dielectric boundary points 31526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 16291 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) : 0.6383360 object centre at (A) : 13.28450 -2.597000 24.16200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0449251E-02 -4.7789379E-03 midg,1,midg; midg,igrid,midg 4.2551689E-02 2.3292411E-02 1,midg,midg; igrid,midg,midg 1.8390991E-02 4.1229229E-02 gauss-seidel spectral radius is 0.9986231 estimated iterations to convergence 214 setup time was (sec) 0.5300000 now iterating at: 11:53:07 rms-change max change #iterations 3.825269 176.6040 at 10iterations 1.778378 67.35561 at 20iterations 0.8286653 26.86373 at 30iterations 0.3838056 13.05886 at 40iterations 0.1789471 5.728840 at 50iterations 8.3214477E-02 2.780301 at 60iterations 3.8823597E-02 1.296338 at 70iterations 1.8072369E-02 0.7816467 at 80iterations 8.3940653E-03 0.2907648 at 90iterations 3.9203661E-03 0.1375613 at 100iterations 1.8314748E-03 6.2446594E-02 at 110iterations 8.5407554E-04 2.7336121E-02 at 120iterations finished qdiffx linear iterations at : 11:53:14 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 8.5407554E-04 2.7336121E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 11:53:15 7.721u 0.214s 0:08.20 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 Sat Oct 15 2011 at 11:53:15 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.872512 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): -13.14000 39.70900 ymin,ymax (A): -30.48200 25.28800 zmin,zma (A): 3.054000 45.27000 x,y,z range (A): 52.84900 55.77000 42.21600 scale (grids/A): 2.872512 object centre (A): 13.28450 -2.597000 24.16200 number of atom coordinates read : 2204 total number of charged atoms : 2070 net assigned charge : 8.000025 assigned positive charge : 319.2597 centred at (gu) : 94.09689 94.56988 84.44403 assigned negative charge : -311.2602 centred at (gu) : 93.81629 94.72753 84.96630 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 153509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21527 grid for indexing accessible points = 1.400000 m= 75561 mr = 106408 m= 27536 mr = 60004 m= 6588 mr = 21456 m= 975 mr = 4666 m= 68 mr = 628 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1120 time to turn everything in is 0.8500000 number of dielectric boundary points 71055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 16558 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) : 1.915008 object centre at (A) : 13.28450 -2.597000 24.16200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3164728 -4.0159788E-02 midg,1,midg; midg,igrid,midg 0.6167030 0.3094682 1,midg,midg; igrid,midg,midg 0.2130314 0.4062475 gauss-seidel spectral radius is 0.9992621 estimated iterations to convergence 291 setup time was (sec) 1.090000 now iterating at: 11:53:16 rms-change max change #iterations 9.178798 397.6108 at 10iterations 5.413207 204.8840 at 20iterations 3.166905 76.75340 at 30iterations 1.844040 40.79405 at 40iterations 1.073322 25.50932 at 50iterations 0.6205292 12.95742 at 60iterations 0.3585446 7.741167 at 70iterations 0.2067322 4.158619 at 80iterations 0.1190953 2.393258 at 90iterations 6.8996266E-02 1.355256 at 100iterations 3.9779648E-02 0.8499041 at 110iterations 2.2858081E-02 0.4601154 at 120iterations 1.3150393E-02 0.2635193 at 130iterations 7.5472137E-03 0.1523631 at 140iterations 4.3422016E-03 7.8872681E-02 at 150iterations 2.4939289E-03 5.4722905E-02 at 160iterations 1.4325524E-03 2.8856635E-02 at 170iterations 8.2348654E-04 1.6872406E-02 at 180iterations finished qdiffx linear iterations at : 11:53:27 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 8.2348654E-04 1.6872406E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 11:53:28 12.457u 0.198s 0:13.00 97.2% 0+0k 0+0io 0pf+0w