Sun Oct 9 01:49:14 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 Sun Oct 9 2011 at 01:49:14 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6659682 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): -27.15800 26.29800 ymin,ymax (A): 8.387000 50.73200 zmin,zma (A): -12.48300 39.82200 x,y,z range (A): 53.45600 42.34500 52.30500 scale (grids/A): 0.6659682 object centre (A): -0.4299994 29.55950 13.66950 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 11.01402 assigned positive charge : 340.5583 centred at (gu) : 90.39184 91.25542 91.66213 assigned negative charge : -329.5450 centred at (gu) : 90.42675 91.19938 91.62566 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7169 nv = 96 ne = 84 npr = 46485 no. pairs analyzed = 46485 no. exposed pairs = 3069 no. arc points = 21968 no. surface atoms = 1032 nbur = 1292 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 3831 m= 6 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3300000 number of dielectric boundary points 3738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2021 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8192 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8363204E-08 5.5384678E-08 midg,1,midg; midg,igrid,midg 1.6896934E-08 5.5891530E-08 1,midg,midg; igrid,midg,midg 3.6266236E-08 2.7683035E-08 gauss-seidel spectral radius is 0.9882966 estimated iterations to convergence 75 setup time was (sec) 0.6000000 now iterating at: 01:49:15 rms-change max change #iterations 0.1621427 24.18352 at 10iterations 1.7285934E-02 2.552312 at 20iterations 1.9806030E-03 0.2724972 at 30iterations 3.0231330E-04 4.8802853E-02 at 40iterations 7.8167468E-05 1.4463425E-02 at 50iterations finished qdiffx linear iterations at : 01:49:18 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 7.8167468E-05 1.4463425E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 01:49:19 4.181u 0.237s 0:04.76 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 01:49:19 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.997905 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): -27.15800 26.29800 ymin,ymax (A): 8.387000 50.73200 zmin,zma (A): -12.48300 39.82200 x,y,z range (A): 53.45600 42.34500 52.30500 scale (grids/A): 1.997905 object centre (A): -0.4299994 29.55950 13.66950 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 11.01402 assigned positive charge : 340.5583 centred at (gu) : 91.17496 93.76587 94.98634 assigned negative charge : -329.5450 centred at (gu) : 91.28034 93.59824 94.87701 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21968 grid for indexing accessible points = 1.400000 m= 28163 mr = 51010 m= 5284 mr = 20587 m= 438 mr = 3449 m= 4 mr = 184 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 562 time to turn everything in is 0.6800000 number of dielectric boundary points 34325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 17331 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) : 0.6659682 object centre at (A) : -0.4299994 29.55950 13.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2837042E-02 3.9860472E-02 midg,1,midg; midg,igrid,midg 3.5325408E-03 3.3857420E-02 1,midg,midg; igrid,midg,midg 6.1765466E-02 5.9533719E-02 gauss-seidel spectral radius is 0.9987361 estimated iterations to convergence 223 setup time was (sec) 1.010000 now iterating at: 01:49:20 rms-change max change #iterations 4.280852 206.2907 at 10iterations 2.060608 75.24204 at 20iterations 0.9885300 31.46951 at 30iterations 0.4761310 14.81279 at 40iterations 0.2284418 7.511853 at 50iterations 0.1101814 3.456696 at 60iterations 5.3192746E-02 1.528503 at 70iterations 2.5641568E-02 0.8892975 at 80iterations 1.2393566E-02 0.3964884 at 90iterations 5.9738699E-03 0.1864824 at 100iterations 2.9095933E-03 9.2481613E-02 at 110iterations 1.4385879E-03 4.6175003E-02 at 120iterations finished qdiffx linear iterations at : 01:49:28 total time elapsed so far: 9.480000 # loops : 120 mean,max change (kT/e) : 1.4385879E-03 4.6175003E-02 energy calculations done at 9.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 01:49:29 9.691u 0.262s 0:10.24 97.1% 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 01:49:29 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2324 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.996857 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): -27.15800 26.29800 ymin,ymax (A): 8.387000 50.73200 zmin,zma (A): -12.48300 39.82200 x,y,z range (A): 53.45600 42.34500 52.30500 scale (grids/A): 2.996857 object centre (A): -0.4299994 29.55950 13.66950 number of atom coordinates read : 2324 total number of charged atoms : 2189 net assigned charge : 11.01402 assigned positive charge : 340.5583 centred at (gu) : 91.76225 95.64867 97.47939 assigned negative charge : -329.5450 centred at (gu) : 91.92049 95.39740 97.31548 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 174987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21968 grid for indexing accessible points = 1.400000 m= 88379 mr = 124167 m= 34755 mr = 71604 m= 9826 mr = 27940 m= 1908 mr = 7526 m= 122 mr = 1360 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1871 time to turn everything in is 1.630000 number of dielectric boundary points 77346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 17511 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) : 1.997905 object centre at (A) : -0.4299994 29.55950 13.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5042434 0.3926371 midg,1,midg; midg,igrid,midg 6.6940654E-03 0.3031896 1,midg,midg; igrid,midg,midg 0.5804742 0.5963501 gauss-seidel spectral radius is 0.9992924 estimated iterations to convergence 297 setup time was (sec) 2.000000 now iterating at: 01:49:31 rms-change max change #iterations 10.01158 407.3215 at 10iterations 5.932556 141.2729 at 20iterations 3.508054 71.83156 at 30iterations 2.069045 43.45463 at 40iterations 1.216729 25.64731 at 50iterations 0.7139152 13.87959 at 60iterations 0.4185532 8.299834 at 70iterations 0.2451843 4.422239 at 80iterations 0.1433305 2.761367 at 90iterations 8.3870031E-02 1.596521 at 100iterations 4.8907116E-02 0.9370174 at 110iterations 2.8609036E-02 0.5421517 at 120iterations 1.6711231E-02 0.3062878 at 130iterations 9.7771101E-03 0.1690788 at 140iterations 5.7257325E-03 0.1112022 at 150iterations 3.3808604E-03 6.4380169E-02 at 160iterations 2.0137071E-03 3.9394379E-02 at 170iterations 1.2280274E-03 2.3452759E-02 at 180iterations finished qdiffx linear iterations at : 01:49:46 total time elapsed so far: 16.57000 # loops : 180 mean,max change (kT/e) : 1.2280274E-03 2.3452759E-02 energy calculations done at 16.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.78000 DelPhi exited at 01:49:47 16.785u 0.325s 0:17.48 97.8% 0+0k 0+0io 0pf+0w