Sat Oct 8 23:18:12 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 Sat Oct 8 2011 at 23:18:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2201 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6635230 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): -13.26400 40.38900 ymin,ymax (A): 14.12000 66.71000 zmin,zma (A): 1.812000 45.71200 x,y,z range (A): 53.65300 52.59000 43.90000 scale (grids/A): 0.6635230 object centre (A): 13.56250 40.41500 23.76200 number of atom coordinates read : 2201 total number of charged atoms : 2066 net assigned charge : 10.50002 assigned positive charge : 318.2097 centred at (gu) : 89.37579 88.32655 88.82252 assigned negative charge : -307.7102 centred at (gu) : 89.42716 88.32282 88.96701 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6951 nv = 96 ne = 84 npr = 43164 no. pairs analyzed = 43164 no. exposed pairs = 2922 no. arc points = 21482 no. surface atoms = 973 nbur = 1228 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3674 m= 8 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.1700000 number of dielectric boundary points 3642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2039 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7789 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7792563E-08 3.2768608E-09 midg,1,midg; midg,igrid,midg 3.9508855E-08 2.1186096E-08 1,midg,midg; igrid,midg,midg 4.2663139E-08 1.7751676E-08 gauss-seidel spectral radius is 0.9882040 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 23:18:13 rms-change max change #iterations 0.1521676 25.66386 at 10iterations 1.6131097E-02 2.346571 at 20iterations 1.7314688E-03 0.2229042 at 30iterations 1.9905754E-04 3.4194946E-02 at 40iterations 2.7441291E-05 4.1465759E-03 at 50iterations finished qdiffx linear iterations at : 23:18:16 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 2.7441291E-05 4.1465759E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 23:18:16 3.597u 0.220s 0:04.09 93.1% 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 Sat Oct 8 2011 at 23:18:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2201 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.990569 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): -13.26400 40.38900 ymin,ymax (A): 14.12000 66.71000 zmin,zma (A): 1.812000 45.71200 x,y,z range (A): 53.65300 52.59000 43.90000 scale (grids/A): 1.990569 object centre (A): 13.56250 40.41500 23.76200 number of atom coordinates read : 2201 total number of charged atoms : 2066 net assigned charge : 10.50002 assigned positive charge : 318.2097 centred at (gu) : 88.12717 84.97971 86.46731 assigned negative charge : -307.7102 centred at (gu) : 88.28143 84.96875 86.90130 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21482 grid for indexing accessible points = 1.400000 m= 27743 mr = 49726 m= 4993 mr = 20303 m= 346 mr = 3214 m= 4 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1866 time to turn everything in is 0.3700000 number of dielectric boundary points 33397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16353 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) : 0.6635230 object centre at (A) : 13.56250 40.41500 23.76200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6925167E-02 -1.0479851E-02 midg,1,midg; midg,igrid,midg 3.2093082E-02 4.4261958E-02 1,midg,midg; igrid,midg,midg 7.2196640E-02 2.3390688E-02 gauss-seidel spectral radius is 0.9987215 estimated iterations to convergence 222 setup time was (sec) 0.6100000 now iterating at: 23:18:17 rms-change max change #iterations 4.084225 196.4071 at 10iterations 1.952144 68.47025 at 20iterations 0.9316030 30.92681 at 30iterations 0.4453413 15.58111 at 40iterations 0.2141546 6.713079 at 50iterations 0.1024417 3.379976 at 60iterations 4.9241170E-02 1.522713 at 70iterations 2.3544120E-02 0.7252965 at 80iterations 1.1309717E-02 0.3548045 at 90iterations 5.4260404E-03 0.1833134 at 100iterations 2.6044981E-03 9.6126556E-02 at 110iterations 1.2526897E-03 4.3909073E-02 at 120iterations finished qdiffx linear iterations at : 23:18:24 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 1.2526897E-03 4.3909073E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 23:18:25 8.119u 0.195s 0:08.60 96.5% 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 Sat Oct 8 2011 at 23:18:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2201 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.985853 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): -13.26400 40.38900 ymin,ymax (A): 14.12000 66.71000 zmin,zma (A): 1.812000 45.71200 x,y,z range (A): 53.65300 52.59000 43.90000 scale (grids/A): 2.985853 object centre (A): 13.56250 40.41500 23.76200 number of atom coordinates read : 2201 total number of charged atoms : 2066 net assigned charge : 10.50002 assigned positive charge : 318.2097 centred at (gu) : 87.19077 82.46954 84.70087 assigned negative charge : -307.7102 centred at (gu) : 87.42209 82.45302 85.35206 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 169679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21482 grid for indexing accessible points = 1.400000 m= 87105 mr = 120278 m= 33907 mr = 70588 m= 9252 mr = 27403 m= 1581 mr = 6981 m= 88 mr = 1037 m= 0 mr = 25 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 5834 time to turn everything in is 0.9500000 number of dielectric boundary points 75300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 16528 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) : 1.990569 object centre at (A) : 13.56250 40.41500 23.76200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2943102 -0.1149583 midg,1,midg; midg,igrid,midg 0.3273598 0.4625586 1,midg,midg; igrid,midg,midg 0.6781631 0.2085137 gauss-seidel spectral radius is 0.9992873 estimated iterations to convergence 296 setup time was (sec) 1.200000 now iterating at: 23:18:26 rms-change max change #iterations 9.584623 365.3055 at 10iterations 5.682077 132.2157 at 20iterations 3.356411 86.33268 at 30iterations 1.975137 43.63609 at 40iterations 1.161094 24.83666 at 50iterations 0.6800932 14.93992 at 60iterations 0.3975616 8.130096 at 70iterations 0.2320925 4.974876 at 80iterations 0.1356347 2.505447 at 90iterations 7.8821294E-02 1.753206 at 100iterations 4.6112239E-02 0.8857536 at 110iterations 2.6808461E-02 0.5194025 at 120iterations 1.5609924E-02 0.3307471 at 130iterations 9.0833232E-03 0.1744576 at 140iterations 5.2880296E-03 0.1020088 at 150iterations 3.0815653E-03 6.5624237E-02 at 160iterations 1.8038781E-03 3.5916328E-02 at 170iterations 1.0608769E-03 2.0847321E-02 at 180iterations finished qdiffx linear iterations at : 23:18:39 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 1.0608769E-03 2.0847321E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 23:18:39 13.766u 0.250s 0:14.29 98.0% 0+0k 0+0io 0pf+0w