Mon Oct 10 14:03:33 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 14:03:33 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5517 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 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= 0.2100000 grid size : 179 scale,in grids/A, set to be: 0.5060555 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): 8.033999 61.68000 ymin,ymax (A): 56.18900 126.5370 zmin,zma (A): 28.98200 96.61400 x,y,z range (A): 53.64600 70.34801 67.63200 scale (grids/A): 0.5060555 object centre (A): 34.85700 91.36300 62.79800 number of atom coordinates read : 5517 total number of charged atoms : 5351 net assigned charge : 4.100031 assigned positive charge : 858.5742 centred at (gu) : 89.58277 89.56145 90.63676 assigned negative charge : -854.4819 centred at (gu) : 89.59716 89.53461 90.51350 start vw surface at 0.2900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 8427 nv = 96 ne = 84 npr = 112752 no. pairs analyzed = 112752 no. exposed pairs = 6614 no. arc points = 45456 no. surface atoms = 2223 nbur = 3294 mkacc time = 0.2600000 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= 297 mr = 4438 m= 0 mr = 5 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.6100000 number of dielectric boundary points 4281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4336 ## 668 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 11628 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3086007E-10 4.2119888E-10 midg,1,midg; midg,igrid,midg -2.6476262E-11 1.0127441E-10 1,midg,midg; igrid,midg,midg 9.1683917E-11 7.9690031E-12 gauss-seidel spectral radius is 0.9800683 estimated iterations to convergence 59 setup time was (sec) 0.8500000 now iterating at: 14:03:34 rms-change max change #iterations 7.0140965E-02 11.08892 at 10iterations 4.9998015E-03 0.6826897 at 20iterations 9.3034556E-04 0.1195202 at 30iterations 2.9947417E-04 4.0474892E-02 at 40iterations 1.0145373E-04 1.4836311E-02 at 50iterations finished qdiffx linear iterations at : 14:03:37 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 1.0145373E-04 1.4836311E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 14:03:38 3.735u 0.143s 0:05.60 69.1% 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 Mon Oct 10 2011 at 14:03:38 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5517 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 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: 1.518167 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): 8.033999 61.68000 ymin,ymax (A): 56.18900 126.5370 zmin,zma (A): 28.98200 96.61400 x,y,z range (A): 53.64600 70.34801 67.63200 scale (grids/A): 1.518167 object centre (A): 34.85700 91.36300 62.79800 number of atom coordinates read : 5517 total number of charged atoms : 5351 net assigned charge : 4.100031 assigned positive charge : 858.5742 centred at (gu) : 88.74661 88.68255 91.90837 assigned negative charge : -854.4819 centred at (gu) : 88.79153 88.60332 91.54063 start vw surface at 0.2300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 96569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45456 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27033 mr = 66935 m= 2235 mr = 18014 m= 52 mr = 925 m= 0 mr = 3 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1800 time to turn everything in is 0.7100000 number of dielectric boundary points 40012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 666 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 39948 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) : 0.5060555 object centre at (A) : 34.85700 91.36300 62.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5700249E-02 1.3214380E-02 midg,1,midg; midg,igrid,midg -9.7785760E-03 5.0843391E-04 1,midg,midg; igrid,midg,midg 4.1387081E-03 3.5044560E-03 gauss-seidel spectral radius is 0.9981194 estimated iterations to convergence 183 setup time was (sec) 1.030000 now iterating at: 14:03:40 rms-change max change #iterations 4.118468 150.8396 at 10iterations 1.686428 60.01417 at 20iterations 0.6917183 22.04710 at 30iterations 0.2861035 8.409455 at 40iterations 0.1172200 4.153385 at 50iterations 4.8489761E-02 1.380680 at 60iterations 2.0098433E-02 0.5992985 at 70iterations 8.3957566E-03 0.2518920 at 80iterations 3.6054309E-03 0.1043205 at 90iterations 1.6491476E-03 5.1406860E-02 at 100iterations 8.1943389E-04 2.6922345E-02 at 110iterations 4.5955760E-04 1.3992310E-02 at 120iterations finished qdiffx linear iterations at : 14:03:47 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 4.5955760E-04 1.3992310E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 14:03:47 8.275u 0.200s 0:09.06 93.4% 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 14:03:48 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5517 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.277250 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): 8.033999 61.68000 ymin,ymax (A): 56.18900 126.5370 zmin,zma (A): 28.98200 96.61400 x,y,z range (A): 53.64600 70.34801 67.63200 scale (grids/A): 2.277250 object centre (A): 34.85700 91.36300 62.79800 number of atom coordinates read : 5517 total number of charged atoms : 5351 net assigned charge : 4.100031 assigned positive charge : 858.5742 centred at (gu) : 88.11928 88.02325 92.86193 assigned negative charge : -854.4819 centred at (gu) : 88.18719 87.90523 92.31082 start vw surface at 0.2400000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 225859 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45456 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 98093 mr = 165230 m= 23893 mr = 76412 m= 3119 mr = 17204 m= 167 mr = 1814 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 5857 time to turn everything in is 1.670000 number of dielectric boundary points 90414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 42669 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) : 1.518167 object centre at (A) : 34.85700 91.36300 62.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2322311 7.3305719E-02 midg,1,midg; midg,igrid,midg -7.3977411E-02 -3.9384919E-03 1,midg,midg; igrid,midg,midg 7.8787312E-02 7.0796497E-02 gauss-seidel spectral radius is 0.9991718 estimated iterations to convergence 274 setup time was (sec) 1.980000 now iterating at: 14:03:50 rms-change max change #iterations 11.17968 273.1847 at 10iterations 6.363279 143.1287 at 20iterations 3.617751 92.52231 at 30iterations 2.045322 41.06424 at 40iterations 1.153403 23.35577 at 50iterations 0.6489263 12.19310 at 60iterations 0.3646395 8.256229 at 70iterations 0.2045890 3.956730 at 80iterations 0.1144850 2.113156 at 90iterations 6.4001270E-02 1.220934 at 100iterations 3.5757173E-02 0.6422234 at 110iterations 1.9959249E-02 0.3450613 at 120iterations 1.1163116E-02 0.2166367 at 130iterations 6.2413150E-03 0.1191177 at 140iterations 3.4979389E-03 6.5757751E-02 at 150iterations 1.9670024E-03 3.8898468E-02 at 160iterations 1.1159593E-03 2.0462036E-02 at 170iterations 6.4154138E-04 1.1920452E-02 at 180iterations finished qdiffx linear iterations at : 14:04:01 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 6.4154138E-04 1.1920452E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 14:04:01 13.394u 0.178s 0:13.93 97.3% 0+0k 0+0io 0pf+0w