Mon Oct 10 00:25:32 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 00:25:32 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 = 5325 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: 0.5042493 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): -25.86900 31.91900 ymin,ymax (A): -22.44200 48.15800 zmin,zma (A): -5.530000 59.02700 x,y,z range (A): 57.78800 70.60000 64.55700 scale (grids/A): 0.5042493 object centre (A): 3.025001 12.85800 26.74850 number of atom coordinates read : 5325 total number of charged atoms : 5174 net assigned charge : -12.99999 assigned positive charge : 792.6129 centred at (gu) : 89.80088 89.23454 90.26080 assigned negative charge : -805.6198 centred at (gu) : 89.77269 89.40485 90.20604 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8389 nv = 96 ne = 84 npr = 109450 no. pairs analyzed = 109450 no. exposed pairs = 6802 no. arc points = 45623 no. surface atoms = 2298 nbur = 3027 mkacc time = 0.2900000 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= 345 mr = 4324 m= 0 mr = 7 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4375 ## 603 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11415 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4671395E-10 -2.1803000E-11 midg,1,midg; midg,igrid,midg 2.8291341E-10 -4.3154277E-10 1,midg,midg; igrid,midg,midg -2.1556608E-10 -7.5317683E-11 gauss-seidel spectral radius is 0.9799249 estimated iterations to convergence 58 setup time was (sec) 0.8200000 now iterating at: 00:25:33 rms-change max change #iterations 6.6071965E-02 12.64926 at 10iterations 4.1973405E-03 0.6755142 at 20iterations 5.9366086E-04 9.7572327E-02 at 30iterations 1.6542702E-04 2.3479462E-02 at 40iterations 5.5040749E-05 7.3742867E-03 at 50iterations finished qdiffx linear iterations at : 00:25:37 total time elapsed so far: 4.780000 # loops : 50 mean,max change (kT/e) : 5.5040749E-05 7.3742867E-03 energy calculations done at 4.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.950000 DelPhi exited at 00:25:38 4.958u 0.406s 0:05.64 94.8% 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 00:25:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5325 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: 1.512748 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): -25.86900 31.91900 ymin,ymax (A): -22.44200 48.15800 zmin,zma (A): -5.530000 59.02700 x,y,z range (A): 57.78800 70.60000 64.55700 scale (grids/A): 1.512748 object centre (A): 3.025001 12.85800 26.74850 number of atom coordinates read : 5325 total number of charged atoms : 5174 net assigned charge : -12.99999 assigned positive charge : 792.6129 centred at (gu) : 89.40102 87.70164 90.78079 assigned negative charge : -805.6198 centred at (gu) : 89.31763 88.21452 90.61755 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 95598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45623 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27894 mr = 65841 m= 2536 mr = 18178 m= 62 mr = 1094 m= 0 mr = 1 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 377 time to turn everything in is 0.8300000 number of dielectric boundary points 40976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 552 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 38610 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) : 0.5042493 object centre at (A) : 3.025001 12.85800 26.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1449734E-03 -2.4319403E-03 midg,1,midg; midg,igrid,midg 2.0895405E-02 -2.4813216E-02 1,midg,midg; igrid,midg,midg -1.4255794E-02 2.6410862E-04 gauss-seidel spectral radius is 0.9980987 estimated iterations to convergence 182 setup time was (sec) 1.170000 now iterating at: 00:25:39 rms-change max change #iterations 3.919989 148.3743 at 10iterations 1.595835 62.60143 at 20iterations 0.6547561 22.42391 at 30iterations 0.2670859 8.817146 at 40iterations 0.1094386 3.604042 at 50iterations 4.5013458E-02 1.537995 at 60iterations 1.8518552E-02 0.5533752 at 70iterations 7.6226662E-03 0.2351913 at 80iterations 3.1664108E-03 9.6772194E-02 at 90iterations 1.3376019E-03 4.3713570E-02 at 100iterations 5.8493362E-04 1.7274976E-02 at 110iterations 2.7743203E-04 9.0255737E-03 at 120iterations finished qdiffx linear iterations at : 00:25:51 total time elapsed so far: 12.74000 # loops : 120 mean,max change (kT/e) : 2.7743203E-04 9.0255737E-03 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 00:25:51 12.915u 0.495s 0:13.77 97.3% 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 00:25:51 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 = 5325 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: 2.269122 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): -25.86900 31.91900 ymin,ymax (A): -22.44200 48.15800 zmin,zma (A): -5.530000 59.02700 x,y,z range (A): 57.78800 70.60000 64.55700 scale (grids/A): 2.269122 object centre (A): 3.025001 12.85800 26.74850 number of atom coordinates read : 5325 total number of charged atoms : 5174 net assigned charge : -12.99999 assigned positive charge : 792.6129 centred at (gu) : 89.10098 86.55196 91.17073 assigned negative charge : -805.6198 centred at (gu) : 88.97638 87.32172 90.92628 start vw surface at 0.1900000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 223009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45623 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 99264 mr = 162304 m= 25755 mr = 76664 m= 3717 mr = 18185 m= 193 mr = 2268 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 1357 time to turn everything in is 2.000000 number of dielectric boundary points 92470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 41278 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) : 1.512748 object centre at (A) : 3.025001 12.85800 26.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1525884 -8.4763944E-02 midg,1,midg; midg,igrid,midg 0.5769441 -0.4097321 1,midg,midg; igrid,midg,midg -0.2964598 4.1538965E-02 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 2.380000 now iterating at: 00:25:54 rms-change max change #iterations 10.83029 323.1900 at 10iterations 6.272091 136.9049 at 20iterations 3.596396 84.32872 at 30iterations 2.054528 42.10696 at 40iterations 1.165776 23.53526 at 50iterations 0.6591668 13.42317 at 60iterations 0.3714183 7.644096 at 70iterations 0.2091367 4.322715 at 80iterations 0.1172739 2.208504 at 90iterations 6.5718144E-02 1.276348 at 100iterations 3.6887478E-02 0.6454754 at 110iterations 2.0629039E-02 0.3598633 at 120iterations 1.1523089E-02 0.2148952 at 130iterations 6.4492673E-03 0.1175900 at 140iterations 3.6082668E-03 6.7097664E-02 at 150iterations 2.0193313E-03 3.6966324E-02 at 160iterations 1.1344943E-03 2.3169041E-02 at 170iterations 6.3809677E-04 1.1047363E-02 at 180iterations finished qdiffx linear iterations at : 00:26:13 total time elapsed so far: 21.07000 # loops : 180 mean,max change (kT/e) : 6.3809677E-04 1.1047363E-02 energy calculations done at 21.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.25000 DelPhi exited at 00:26:14 21.253u 0.524s 0:22.20 98.0% 0+0k 0+0io 0pf+0w