Tue Oct 11 03:18:59 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 Tue Oct 11 2011 at 03:18:59 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 = 2244 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: 0.5727524 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): -12.03000 37.61500 ymin,ymax (A): -52.63200 -7.882000 zmin,zma (A): -5.097000 57.05900 x,y,z range (A): 49.64500 44.75000 62.15600 scale (grids/A): 0.5727524 object centre (A): 12.79250 -30.25700 25.98100 number of atom coordinates read : 2244 total number of charged atoms : 2102 net assigned charge : 4.500031 assigned positive charge : 326.0487 centred at (gu) : 88.48950 89.72067 88.81849 assigned negative charge : -321.5492 centred at (gu) : 88.36956 89.77789 88.78413 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4924 nv = 96 ne = 84 npr = 44311 no. pairs analyzed = 44311 no. exposed pairs = 3160 no. arc points = 22284 no. surface atoms = 1058 nbur = 1186 mkacc time = 0.1200000 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 = 1.484000 m= 215 mr = 2353 m= 0 mr = 13 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2216 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6208 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6543194E-10 9.2269142E-10 midg,1,midg; midg,igrid,midg 1.5964740E-09 7.0347464E-11 1,midg,midg; igrid,midg,midg -1.0656167E-09 1.5834480E-09 gauss-seidel spectral radius is 0.9842160 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 03:19:00 rms-change max change #iterations 7.7079952E-02 13.97722 at 10iterations 5.7504508E-03 1.076275 at 20iterations 4.3885122E-04 7.7704906E-02 at 30iterations 3.4133544E-05 6.0119629E-03 at 40iterations 3.1917889E-06 5.7601929E-04 at 50iterations finished qdiffx linear iterations at : 03:19:04 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 3.1917889E-06 5.7601929E-04 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.350000 DelPhi exited at 03:19:05 5.355u 0.421s 0:06.18 93.3% 0+0k 0+0io 6pf+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 03:19:05 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 = 2244 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: 1.718257 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): -12.03000 37.61500 ymin,ymax (A): -52.63200 -7.882000 zmin,zma (A): -5.097000 57.05900 x,y,z range (A): 49.64500 44.75000 62.15600 scale (grids/A): 1.718257 object centre (A): 12.79250 -30.25700 25.98100 number of atom coordinates read : 2244 total number of charged atoms : 2102 net assigned charge : 4.500031 assigned positive charge : 326.0487 centred at (gu) : 85.46819 89.16176 86.45522 assigned negative charge : -321.5492 centred at (gu) : 85.10867 89.33386 86.35249 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 53195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22284 grid for indexing accessible points = 1.400000 m= 16720 mr = 34135 m= 1893 mr = 11214 m= 79 mr = 884 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 25648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 16294 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) : 0.5727524 object centre at (A) : 12.79250 -30.25700 25.98100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1218592E-03 -3.8107610E-04 midg,1,midg; midg,igrid,midg 4.7348300E-03 -2.8242324E-03 1,midg,midg; igrid,midg,midg 2.3319074E-03 9.8821959E-03 gauss-seidel spectral radius is 0.9982908 estimated iterations to convergence 192 setup time was (sec) 0.8200000 now iterating at: 03:19:06 rms-change max change #iterations 3.085959 172.3635 at 10iterations 1.308941 58.13728 at 20iterations 0.5596967 23.48458 at 30iterations 0.2386479 9.118162 at 40iterations 0.1018808 3.738518 at 50iterations 4.3644749E-02 1.585819 at 60iterations 1.8609343E-02 0.7467575 at 70iterations 7.9568848E-03 0.3299103 at 80iterations 3.4117138E-03 0.1373444 at 90iterations 1.4494807E-03 5.4250002E-02 at 100iterations 6.2207703E-04 2.5417328E-02 at 110iterations 2.6643160E-04 1.0057926E-02 at 120iterations finished qdiffx linear iterations at : 03:19:17 total time elapsed so far: 11.81000 # loops : 120 mean,max change (kT/e) : 2.6643160E-04 1.0057926E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 03:19:18 12.017u 0.462s 0:13.02 95.7% 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 03:19:18 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 = 2244 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: 2.577386 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): -12.03000 37.61500 ymin,ymax (A): -52.63200 -7.882000 zmin,zma (A): -5.097000 57.05900 x,y,z range (A): 49.64500 44.75000 62.15600 scale (grids/A): 2.577386 object centre (A): 12.79250 -30.25700 25.98100 number of atom coordinates read : 2244 total number of charged atoms : 2102 net assigned charge : 4.500031 assigned positive charge : 326.0487 centred at (gu) : 83.20222 88.74257 84.68272 assigned negative charge : -321.5492 centred at (gu) : 82.66313 89.00075 84.52871 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 123244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22284 grid for indexing accessible points = 1.400000 m= 56419 mr = 83684 m= 16942 mr = 43732 m= 3029 mr = 12493 m= 288 mr = 1887 m= 11 mr = 127 m= 0 mr = 1 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 58009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 16810 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) : 1.718257 object centre at (A) : 12.79250 -30.25700 25.98100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2087132 0.1618405 midg,1,midg; midg,igrid,midg 4.2922359E-02 -5.1694244E-02 1,midg,midg; igrid,midg,midg 2.0829616E-02 0.1100594 gauss-seidel spectral radius is 0.9991577 estimated iterations to convergence 272 setup time was (sec) 1.490000 now iterating at: 03:19:20 rms-change max change #iterations 7.782125 261.8085 at 10iterations 4.401043 139.1205 at 20iterations 2.473886 67.94202 at 30iterations 1.384404 55.78856 at 40iterations 0.7716448 21.71939 at 50iterations 0.4302956 11.16648 at 60iterations 0.2391050 5.409058 at 70iterations 0.1328990 3.276058 at 80iterations 7.3596396E-02 1.632763 at 90iterations 4.0830929E-02 0.9634098 at 100iterations 2.2601800E-02 0.6398010 at 110iterations 1.2538820E-02 0.2964354 at 120iterations 6.9480031E-03 0.1582031 at 130iterations 3.8488063E-03 8.3092690E-02 at 140iterations 2.1272050E-03 5.0048828E-02 at 150iterations 1.1775700E-03 2.9801369E-02 at 160iterations 6.5351394E-04 1.5537262E-02 at 170iterations 3.6256079E-04 7.5912476E-03 at 180iterations finished qdiffx linear iterations at : 03:19:39 total time elapsed so far: 20.02000 # loops : 180 mean,max change (kT/e) : 3.6256079E-04 7.5912476E-03 energy calculations done at 20.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.17000 DelPhi exited at 03:19:39 20.173u 0.520s 0:21.02 98.4% 0+0k 0+0io 0pf+0w