Sun Oct 9 00:29:20 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 00:29:20 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3319 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5428981 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): 8.388000 54.90600 ymin,ymax (A): -13.40700 52.16700 zmin,zma (A): -26.27700 34.96800 x,y,z range (A): 46.51800 65.57400 61.24500 scale (grids/A): 0.5428981 object centre (A): 31.64700 19.38000 4.345501 number of atom coordinates read : 3319 total number of charged atoms : 3175 net assigned charge : 9.726042 assigned positive charge : 489.8266 centred at (gu) : 89.90889 90.64600 90.49890 assigned negative charge : -480.1023 centred at (gu) : 89.93038 90.88672 90.64485 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6612 nv = 96 ne = 84 npr = 64121 no. pairs analyzed = 64121 no. exposed pairs = 4522 no. arc points = 32237 no. surface atoms = 1518 nbur = 1801 mkacc time = 0.1100000 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 = 1.568000 m= 310 mr = 3277 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3271 ## 427 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8606 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2994588E-09 -4.5121235E-10 midg,1,midg; midg,igrid,midg 1.7430745E-09 -1.2191076E-09 1,midg,midg; igrid,midg,midg 7.0787465E-10 4.0878664E-10 gauss-seidel spectral radius is 0.9825512 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 00:29:21 rms-change max change #iterations 7.3254846E-02 11.64424 at 10iterations 4.8621316E-03 0.7657394 at 20iterations 3.2955036E-04 5.5809021E-02 at 30iterations 2.6928734E-05 4.0283203E-03 at 40iterations 3.3696674E-06 4.5013428E-04 at 50iterations finished qdiffx linear iterations at : 00:29:24 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.3696674E-06 4.5013428E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 00:29:24 3.415u 0.174s 0:03.87 92.5% 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 Sun Oct 9 2011 at 00:29:24 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3319 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.628694 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): 8.388000 54.90600 ymin,ymax (A): -13.40700 52.16700 zmin,zma (A): -26.27700 34.96800 x,y,z range (A): 46.51800 65.57400 61.24500 scale (grids/A): 1.628694 object centre (A): 31.64700 19.38000 4.345501 number of atom coordinates read : 3319 total number of charged atoms : 3175 net assigned charge : 9.726042 assigned positive charge : 489.8266 centred at (gu) : 89.72585 91.93682 91.49577 assigned negative charge : -480.1023 centred at (gu) : 89.79083 92.66007 91.93430 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32237 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23393 mr = 48161 m= 2706 mr = 15843 m= 71 mr = 1351 m= 0 mr = 4 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.3600000 number of dielectric boundary points 33842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 368 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 24313 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) : 0.5428981 object centre at (A) : 31.64700 19.38000 4.345501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9810528E-02 3.7258123E-03 midg,1,midg; midg,igrid,midg 2.1097552E-02 -2.1966597E-02 1,midg,midg; igrid,midg,midg 5.0373874E-03 1.3566927E-02 gauss-seidel spectral radius is 0.9982321 estimated iterations to convergence 189 setup time was (sec) 0.5700000 now iterating at: 00:29:25 rms-change max change #iterations 3.448587 151.2113 at 10iterations 1.450460 56.40944 at 20iterations 0.6104562 21.78381 at 30iterations 0.2561231 8.883865 at 40iterations 0.1075806 3.947601 at 50iterations 4.5431241E-02 1.568009 at 60iterations 1.9216599E-02 0.7426612 at 70iterations 8.1246914E-03 0.3028288 at 80iterations 3.4110437E-03 0.1105804 at 90iterations 1.4370668E-03 5.1237106E-02 at 100iterations 6.0693600E-04 2.1865845E-02 at 110iterations 2.5671977E-04 8.8195801E-03 at 120iterations finished qdiffx linear iterations at : 00:29:32 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.5671977E-04 8.8195801E-03 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 00:29:33 7.716u 0.194s 0:08.33 94.8% 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 00:29:33 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3319 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.443042 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): 8.388000 54.90600 ymin,ymax (A): -13.40700 52.16700 zmin,zma (A): -26.27700 34.96800 x,y,z range (A): 46.51800 65.57400 61.24500 scale (grids/A): 2.443042 object centre (A): 31.64700 19.38000 4.345501 number of atom coordinates read : 3319 total number of charged atoms : 3175 net assigned charge : 9.726042 assigned positive charge : 489.8266 centred at (gu) : 89.58855 92.90499 92.24340 assigned negative charge : -480.1023 centred at (gu) : 89.68621 93.99005 92.90144 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 169443 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32237 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 78909 mr = 118196 m= 24015 mr = 61329 m= 4234 mr = 18171 m= 297 mr = 2820 m= 4 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 1208 time to turn everything in is 0.8700000 number of dielectric boundary points 76254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 25358 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) : 1.628694 object centre at (A) : 31.64700 19.38000 4.345501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2770418 0.1755738 midg,1,midg; midg,igrid,midg 0.1887960 -0.3646718 1,midg,midg; igrid,midg,midg 5.4934498E-02 0.2375044 gauss-seidel spectral radius is 0.9991718 estimated iterations to convergence 274 setup time was (sec) 1.120000 now iterating at: 00:29:34 rms-change max change #iterations 9.129598 278.9682 at 10iterations 5.245673 123.9522 at 20iterations 2.983135 66.37849 at 30iterations 1.690551 38.02958 at 40iterations 0.9513463 19.44831 at 50iterations 0.5345060 10.66476 at 60iterations 0.2987976 6.433765 at 70iterations 0.1670116 3.340698 at 80iterations 9.3184240E-02 1.740995 at 90iterations 5.2074078E-02 1.002380 at 100iterations 2.8947331E-02 0.6029072 at 110iterations 1.6119689E-02 0.2963184 at 120iterations 8.9606745E-03 0.1660953 at 130iterations 4.9997186E-03 9.7602844E-02 at 140iterations 2.7755252E-03 5.0951004E-02 at 150iterations 1.5423498E-03 3.0009270E-02 at 160iterations 8.5758697E-04 1.5954971E-02 at 170iterations 4.7654417E-04 9.1552734E-03 at 180iterations finished qdiffx linear iterations at : 00:29:45 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 4.7654417E-04 9.1552734E-03 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 00:29:46 12.527u 0.192s 0:13.00 97.7% 0+0k 0+0io 0pf+0w