Mon Oct 10 17:01:57 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 17:01:57 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4632 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5133234 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): -15.75200 36.13400 ymin,ymax (A): -30.02400 31.46000 zmin,zma (A): -4.332000 65.02000 x,y,z range (A): 51.88600 61.48400 69.35200 scale (grids/A): 0.5133234 object centre (A): 10.19100 0.7179995 30.34400 number of atom coordinates read : 4632 total number of charged atoms : 4430 net assigned charge : 6.400043 assigned positive charge : 696.6246 centred at (gu) : 89.85626 90.79616 88.36741 assigned negative charge : -690.2291 centred at (gu) : 89.77966 90.86272 88.38779 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7512 nv = 96 ne = 84 npr = 95408 no. pairs analyzed = 95408 no. exposed pairs = 5769 no. arc points = 39667 no. surface atoms = 1935 nbur = 2697 mkacc time = 0.2300000 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 = 1.652000 m= 262 mr = 3874 m= 0 mr = 4 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3937 ## 593 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4548369E-10 3.1081724E-11 midg,1,midg; midg,igrid,midg 2.3411911E-10 -1.0654390E-10 1,midg,midg; igrid,midg,midg -1.1844493E-10 3.0411015E-10 gauss-seidel spectral radius is 0.9805751 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 17:01:58 rms-change max change #iterations 7.0421070E-02 11.90166 at 10iterations 4.0991735E-03 0.7002068 at 20iterations 4.0488827E-04 5.6459427E-02 at 30iterations 1.2943865E-04 1.9426346E-02 at 40iterations 5.0956671E-05 7.5435638E-03 at 50iterations finished qdiffx linear iterations at : 17:02:01 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 5.0956671E-05 7.5435638E-03 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 17:02:03 3.892u 0.196s 0:05.51 74.0% 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 17:02:03 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4632 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.539970 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): -15.75200 36.13400 ymin,ymax (A): -30.02400 31.46000 zmin,zma (A): -4.332000 65.02000 x,y,z range (A): 51.88600 61.48400 69.35200 scale (grids/A): 1.539970 object centre (A): 10.19100 0.7179995 30.34400 number of atom coordinates read : 4632 total number of charged atoms : 4430 net assigned charge : 6.400043 assigned positive charge : 696.6246 centred at (gu) : 89.56746 92.38678 85.10066 assigned negative charge : -690.2291 centred at (gu) : 89.33852 92.58784 85.16321 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 85693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39667 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23777 mr = 58813 m= 2062 mr = 15429 m= 40 mr = 833 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 36497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 556 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 33439 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) : 0.5133234 object centre at (A) : 10.19100 0.7179995 30.34400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8805351E-03 -2.2031032E-03 midg,1,midg; midg,igrid,midg 1.1074934E-02 -6.6800108E-03 1,midg,midg; igrid,midg,midg 1.5406408E-04 8.6970730E-03 gauss-seidel spectral radius is 0.9981149 estimated iterations to convergence 183 setup time was (sec) 0.9300000 now iterating at: 17:02:04 rms-change max change #iterations 3.755365 145.2766 at 10iterations 1.541146 49.93830 at 20iterations 0.6311189 20.08591 at 30iterations 0.2593742 8.408504 at 40iterations 0.1064975 3.775730 at 50iterations 4.3838121E-02 1.426853 at 60iterations 1.8005857E-02 0.6171007 at 70iterations 7.4276305E-03 0.2377105 at 80iterations 3.1046751E-03 9.7954750E-02 at 90iterations 1.3133700E-03 4.1255951E-02 at 100iterations 5.8523874E-04 1.9878387E-02 at 110iterations 2.8939790E-04 1.1029243E-02 at 120iterations finished qdiffx linear iterations at : 17:02:11 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 2.8939790E-04 1.1029243E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 17:02:12 8.136u 0.184s 0:09.28 89.5% 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 Mon Oct 10 2011 at 17:02:12 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4632 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.309955 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): -15.75200 36.13400 ymin,ymax (A): -30.02400 31.46000 zmin,zma (A): -4.332000 65.02000 x,y,z range (A): 51.88600 61.48400 69.35200 scale (grids/A): 2.309955 object centre (A): 10.19100 0.7179995 30.34400 number of atom coordinates read : 4632 total number of charged atoms : 4430 net assigned charge : 6.400043 assigned positive charge : 696.6246 centred at (gu) : 89.35087 93.57986 82.65074 assigned negative charge : -690.2291 centred at (gu) : 89.00769 93.88158 82.74476 start vw surface at 0.2200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 199889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39667 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86483 mr = 144746 m= 21121 mr = 66970 m= 2893 mr = 14734 m= 136 mr = 1677 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.540000 number of dielectric boundary points 82361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 35357 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) : 1.539970 object centre at (A) : 10.19100 0.7179995 30.34400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1499964 -0.1465071 midg,1,midg; midg,igrid,midg 0.1737200 -0.1887196 1,midg,midg; igrid,midg,midg 5.3029316E-03 0.1342567 gauss-seidel spectral radius is 0.9991587 estimated iterations to convergence 272 setup time was (sec) 1.860000 now iterating at: 17:02:14 rms-change max change #iterations 10.14290 270.2841 at 10iterations 5.794700 147.3454 at 20iterations 3.284380 74.95614 at 30iterations 1.852316 39.18803 at 40iterations 1.042793 22.73542 at 50iterations 0.5850993 12.24432 at 60iterations 0.3272536 7.246687 at 70iterations 0.1825138 3.514462 at 80iterations 0.1019454 2.053123 at 90iterations 5.6766130E-02 1.063392 at 100iterations 3.1617593E-02 0.5770378 at 110iterations 1.7595675E-02 0.3780766 at 120iterations 9.7757298E-03 0.1916533 at 130iterations 5.4472252E-03 0.1088676 at 140iterations 3.0369081E-03 5.8891296E-02 at 150iterations 1.6989593E-03 3.4739494E-02 at 160iterations 9.5673668E-04 1.8078804E-02 at 170iterations 5.4877024E-04 1.0639191E-02 at 180iterations finished qdiffx linear iterations at : 17:02:25 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 5.4877024E-04 1.0639191E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 17:02:26 13.191u 0.234s 0:13.81 97.1% 0+0k 0+0io 0pf+0w