Mon Oct 10 17:06:07 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 Mon Oct 10 2011 at 17:06:07 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 !!! WARNING: HEM 825 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5103285 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): -16.44000 37.16000 ymin,ymax (A): -32.77000 31.36100 zmin,zma (A): -3.992000 65.76700 x,y,z range (A): 53.60000 64.13100 69.75900 scale (grids/A): 0.5103285 object centre (A): 10.36000 -0.7045002 30.88750 number of atom coordinates read : 4333 total number of charged atoms : 4089 net assigned charge : 3.300030 assigned positive charge : 644.9702 centred at (gu) : 90.16022 90.96806 87.54857 assigned negative charge : -641.6742 centred at (gu) : 90.02644 90.99677 87.59573 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7174 nv = 96 ne = 84 npr = 88057 no. pairs analyzed = 88057 no. exposed pairs = 5597 no. arc points = 39138 no. surface atoms = 1866 nbur = 2467 mkacc time = 0.2000000 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 = 1.680000 m= 255 mr = 3632 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3733 ## 580 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8998967E-10 -3.3406476E-11 midg,1,midg; midg,igrid,midg 8.4317803E-11 -2.9956957E-11 1,midg,midg; igrid,midg,midg -2.5640945E-10 3.5827541E-10 gauss-seidel spectral radius is 0.9803331 estimated iterations to convergence 59 setup time was (sec) 0.6400000 now iterating at: 17:06:08 rms-change max change #iterations 6.3349403E-02 11.49297 at 10iterations 3.5329636E-03 0.5628777 at 20iterations 2.7284585E-04 3.9104462E-02 at 30iterations 6.4724249E-05 1.0201484E-02 at 40iterations 2.3000981E-05 3.9980412E-03 at 50iterations finished qdiffx linear iterations at : 17:06:10 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 2.3000981E-05 3.9980412E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 17:06:11 3.227u 0.139s 0:03.72 90.0% 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 Mon Oct 10 2011 at 17:06:11 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 = 4333 !!! WARNING: HEM 825 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.530985 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): -16.44000 37.16000 ymin,ymax (A): -32.77000 31.36100 zmin,zma (A): -3.992000 65.76700 x,y,z range (A): 53.60000 64.13100 69.75900 scale (grids/A): 1.530985 object centre (A): 10.36000 -0.7045002 30.88750 number of atom coordinates read : 4333 total number of charged atoms : 4089 net assigned charge : 3.300030 assigned positive charge : 644.9702 centred at (gu) : 90.47890 92.90310 82.64431 assigned negative charge : -641.6742 centred at (gu) : 90.07885 92.98999 82.78718 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39138 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22570 mr = 55224 m= 1848 mr = 14619 m= 46 mr = 687 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.5500000 number of dielectric boundary points 35288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 521 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 30772 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) : 0.5103285 object centre at (A) : 10.36000 -0.7045002 30.88750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1282044E-03 7.7202301E-03 midg,1,midg; midg,igrid,midg -1.3324568E-03 -5.2196006E-03 1,midg,midg; igrid,midg,midg -2.6365146E-03 9.0526063E-03 gauss-seidel spectral radius is 0.9980683 estimated iterations to convergence 181 setup time was (sec) 0.8400000 now iterating at: 17:06:12 rms-change max change #iterations 3.551513 146.7385 at 10iterations 1.432375 53.73655 at 20iterations 0.5792941 20.57939 at 30iterations 0.2352832 8.140059 at 40iterations 9.5514983E-02 3.399258 at 50iterations 3.8809866E-02 1.458158 at 60iterations 1.5775451E-02 0.5126615 at 70iterations 6.3959979E-03 0.2374814 at 80iterations 2.6121929E-03 8.3889008E-02 at 90iterations 1.0609564E-03 3.8160324E-02 at 100iterations 4.3327923E-04 1.5886307E-02 at 110iterations 1.7778830E-04 6.2875748E-03 at 120iterations finished qdiffx linear iterations at : 17:06:18 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 1.7778830E-04 6.2875748E-03 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 17:06:19 7.220u 0.203s 0:07.83 94.7% 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 Mon Oct 10 2011 at 17:06:19 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4333 !!! WARNING: HEM 825 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.296478 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): -16.44000 37.16000 ymin,ymax (A): -32.77000 31.36100 zmin,zma (A): -3.992000 65.76700 x,y,z range (A): 53.60000 64.13100 69.75900 scale (grids/A): 2.296478 object centre (A): 10.36000 -0.7045002 30.88750 number of atom coordinates read : 4333 total number of charged atoms : 4089 net assigned charge : 3.300030 assigned positive charge : 644.9702 centred at (gu) : 90.71796 94.35409 78.96619 assigned negative charge : -641.6742 centred at (gu) : 90.11812 94.48495 79.18076 start vw surface at 0.1900000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 189585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39138 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 82290 mr = 136268 m= 19677 mr = 63407 m= 2555 mr = 13642 m= 135 mr = 1393 m= 0 mr = 38 time to grow re-entrant surface = 0.7699999 no. cavity mid-points inaccessible to solvent = 186 time to turn everything in is 1.330000 number of dielectric boundary points 79494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 32617 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) : 1.530985 object centre at (A) : 10.36000 -0.7045002 30.88750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1497179 0.2424075 midg,1,midg; midg,igrid,midg -9.9537648E-02 -0.1588934 1,midg,midg; igrid,midg,midg -3.0234262E-02 0.1386020 gauss-seidel spectral radius is 0.9991404 estimated iterations to convergence 269 setup time was (sec) 1.620000 now iterating at: 17:06:21 rms-change max change #iterations 9.705095 289.2356 at 10iterations 5.530161 150.7081 at 20iterations 3.128927 72.74014 at 30iterations 1.756405 40.03290 at 40iterations 0.9841731 22.14149 at 50iterations 0.5479793 12.09494 at 60iterations 0.3048263 6.563066 at 70iterations 0.1691046 3.493676 at 80iterations 9.3714215E-02 1.906977 at 90iterations 5.1846586E-02 1.056961 at 100iterations 2.8664671E-02 0.6320066 at 110iterations 1.5870366E-02 0.3238249 at 120iterations 8.7564522E-03 0.1753178 at 130iterations 4.8242225E-03 9.0024948E-02 at 140iterations 2.6627677E-03 5.3550720E-02 at 150iterations 1.4689584E-03 2.7778625E-02 at 160iterations 8.1168214E-04 1.8417358E-02 at 170iterations 4.4934172E-04 9.0546608E-03 at 180iterations finished qdiffx linear iterations at : 17:06:31 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 4.4934172E-04 9.0546608E-03 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 17:06:31 11.700u 0.223s 0:12.62 94.4% 0+0k 0+0io 0pf+0w