Tue Oct 11 08:26:27 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 Tue Oct 11 2011 at 08:26:27 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIQ 69 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6617346 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): -12.86300 36.36300 ymin,ymax (A): -26.90200 20.17800 zmin,zma (A): -8.014000 45.78400 x,y,z range (A): 49.22600 47.08000 53.79800 scale (grids/A): 0.6617346 object centre (A): 11.75000 -3.362000 18.88500 number of atom coordinates read : 2687 total number of charged atoms : 2536 net assigned charge : 4.176027 assigned positive charge : 408.3280 centred at (gu) : 90.73265 90.64689 91.35828 assigned negative charge : -404.1524 centred at (gu) : 90.45102 90.41964 91.25375 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7904 nv = 96 ne = 84 npr = 54725 no. pairs analyzed = 54725 no. exposed pairs = 3231 no. arc points = 22401 no. surface atoms = 1086 nbur = 1601 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 4541 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.3100000 number of dielectric boundary points 3764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2225 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9345 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3774570E-09 4.2931411E-08 midg,1,midg; midg,igrid,midg -3.4806050E-08 6.6195490E-08 1,midg,midg; igrid,midg,midg -4.4744258E-08 8.0350674E-08 gauss-seidel spectral radius is 0.9881681 estimated iterations to convergence 75 setup time was (sec) 0.6000000 now iterating at: 08:26:28 rms-change max change #iterations 0.1788916 22.45981 at 10iterations 1.9380707E-02 2.435196 at 20iterations 2.0999901E-03 0.2548294 at 30iterations 2.2906078E-04 2.9747009E-02 at 40iterations 2.7549338E-05 3.9072037E-03 at 50iterations finished qdiffx linear iterations at : 08:26:32 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.7549338E-05 3.9072037E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 08:26:32 4.095u 0.354s 0:05.06 87.7% 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 Tue Oct 11 2011 at 08:26:33 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIQ 69 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.985204 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): -12.86300 36.36300 ymin,ymax (A): -26.90200 20.17800 zmin,zma (A): -8.014000 45.78400 x,y,z range (A): 49.22600 47.08000 53.79800 scale (grids/A): 1.985204 object centre (A): 11.75000 -3.362000 18.88500 number of atom coordinates read : 2687 total number of charged atoms : 2536 net assigned charge : 4.176027 assigned positive charge : 408.3280 centred at (gu) : 92.19769 91.94011 94.07453 assigned negative charge : -404.1524 centred at (gu) : 91.35271 91.25887 93.76118 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22401 grid for indexing accessible points = 1.400000 m= 33443 mr = 59507 m= 6062 mr = 25597 m= 451 mr = 4083 m= 6 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 2300 time to turn everything in is 0.6600000 number of dielectric boundary points 34598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20027 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) : 0.6617346 object centre at (A) : 11.75000 -3.362000 18.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9443057E-02 7.7879545E-03 midg,1,midg; midg,igrid,midg -1.3960379E-02 5.3939618E-02 1,midg,midg; igrid,midg,midg -1.5197080E-02 9.1360129E-02 gauss-seidel spectral radius is 0.9987452 estimated iterations to convergence 224 setup time was (sec) 0.9500000 now iterating at: 08:26:34 rms-change max change #iterations 4.723434 197.0701 at 10iterations 2.295319 82.70508 at 20iterations 1.104704 35.95103 at 30iterations 0.5365602 15.69695 at 40iterations 0.2599004 7.680866 at 50iterations 0.1259482 4.573650 at 60iterations 6.1067916E-02 1.797577 at 70iterations 2.9528057E-02 0.9247494 at 80iterations 1.4283309E-02 0.3961525 at 90iterations 6.9123590E-03 0.2200050 at 100iterations 3.3509384E-03 0.1002502 at 110iterations 1.6292552E-03 4.8694611E-02 at 120iterations finished qdiffx linear iterations at : 08:26:42 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 1.6292552E-03 4.8694611E-02 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 08:26:43 9.762u 0.421s 0:10.57 96.3% 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 Tue Oct 11 2011 at 08:26:43 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIQ 69 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.977806 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): -12.86300 36.36300 ymin,ymax (A): -26.90200 20.17800 zmin,zma (A): -8.014000 45.78400 x,y,z range (A): 49.22600 47.08000 53.79800 scale (grids/A): 2.977806 object centre (A): 11.75000 -3.362000 18.88500 number of atom coordinates read : 2687 total number of charged atoms : 2536 net assigned charge : 4.176027 assigned positive charge : 408.3280 centred at (gu) : 93.29636 92.91004 96.11166 assigned negative charge : -404.1524 centred at (gu) : 92.02901 91.88819 95.64169 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 193918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22401 grid for indexing accessible points = 1.400000 m= 104674 mr = 143399 m= 42098 mr = 87421 m= 11192 mr = 34948 m= 1824 mr = 8663 m= 140 mr = 1311 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 7741 time to turn everything in is 1.780000 number of dielectric boundary points 78042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 20282 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) : 1.985204 object centre at (A) : 11.75000 -3.362000 18.88500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7169393 0.1924511 midg,1,midg; midg,igrid,midg -0.1555109 0.5798672 1,midg,midg; igrid,midg,midg -0.1691388 0.7864785 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 2.120000 now iterating at: 08:26:46 rms-change max change #iterations 10.89638 419.3047 at 10iterations 6.410057 163.9679 at 20iterations 3.767527 70.42586 at 30iterations 2.217719 47.36163 at 40iterations 1.294176 22.72480 at 50iterations 0.7580274 13.03459 at 60iterations 0.4423878 9.486874 at 70iterations 0.2581377 4.755421 at 80iterations 0.1508935 2.707582 at 90iterations 8.7760486E-02 1.595644 at 100iterations 5.1136140E-02 0.8265743 at 110iterations 2.9693995E-02 0.5066719 at 120iterations 1.7306028E-02 0.2818775 at 130iterations 1.0049056E-02 0.1742039 at 140iterations 5.8721555E-03 9.5756531E-02 at 150iterations 3.4236249E-03 5.7312012E-02 at 160iterations 2.0060258E-03 3.2136917E-02 at 170iterations 1.1800426E-03 2.1425247E-02 at 180iterations finished qdiffx linear iterations at : 08:27:01 total time elapsed so far: 17.06000 # loops : 180 mean,max change (kT/e) : 1.1800426E-03 2.1425247E-02 energy calculations done at 17.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.23000 DelPhi exited at 08:27:01 17.237u 0.454s 0:18.15 97.4% 0+0k 0+0io 0pf+0w