Tue Oct 11 07:50:41 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 07:50:41 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 = 3751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5420879 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): 88.29400 140.0550 ymin,ymax (A): 115.6140 181.2860 zmin,zma (A): -34.23900 23.36400 x,y,z range (A): 51.76099 65.67201 57.60300 scale (grids/A): 0.5420879 object centre (A): 114.1745 148.4500 -5.437501 number of atom coordinates read : 3751 total number of charged atoms : 3604 net assigned charge : 9.500016 assigned positive charge : 572.7215 centred at (gu) : 89.99490 89.67299 90.64266 assigned negative charge : -563.2240 centred at (gu) : 89.96954 89.64780 90.63776 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7251 nv = 96 ne = 84 npr = 72536 no. pairs analyzed = 72536 no. exposed pairs = 4976 no. arc points = 35819 no. surface atoms = 1666 nbur = 2085 mkacc time = 0.1900000 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 = 1.568000 m= 341 mr = 3610 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3957 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3602 ## 489 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0467801E-10 6.3545574E-10 midg,1,midg; midg,igrid,midg 3.4997621E-10 6.3737293E-10 1,midg,midg; igrid,midg,midg 3.2313979E-10 6.9080658E-10 gauss-seidel spectral radius is 0.9825264 estimated iterations to convergence 62 setup time was (sec) 0.7000000 now iterating at: 07:50:42 rms-change max change #iterations 8.0032744E-02 11.20280 at 10iterations 5.6028473E-03 0.8630047 at 20iterations 6.5974944E-04 0.1336861 at 30iterations 1.7645341E-04 3.1974792E-02 at 40iterations 5.6999423E-05 1.0058403E-02 at 50iterations finished qdiffx linear iterations at : 07:50:46 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 5.6999423E-05 1.0058403E-02 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.600000 DelPhi exited at 07:50:47 4.607u 0.400s 0:05.62 88.9% 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 07:50:47 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 = 3751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.626263 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): 88.29400 140.0550 ymin,ymax (A): 115.6140 181.2860 zmin,zma (A): -34.23900 23.36400 x,y,z range (A): 51.76099 65.67201 57.60300 scale (grids/A): 1.626263 object centre (A): 114.1745 148.4500 -5.437501 number of atom coordinates read : 3751 total number of charged atoms : 3604 net assigned charge : 9.500016 assigned positive charge : 572.7215 centred at (gu) : 89.98369 89.01762 91.92686 assigned negative charge : -563.2240 centred at (gu) : 89.90865 88.94284 91.91283 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35819 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26954 mr = 51905 m= 3312 mr = 18920 m= 101 mr = 1707 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 36760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 407 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 27525 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) : 0.5420879 object centre at (A) : 114.1745 148.4500 -5.437501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4702254E-03 1.0017731E-02 midg,1,midg; midg,igrid,midg -1.0298382E-02 2.4934499E-02 1,midg,midg; igrid,midg,midg 1.0504205E-03 7.8371139E-03 gauss-seidel spectral radius is 0.9982647 estimated iterations to convergence 191 setup time was (sec) 0.9800000 now iterating at: 07:50:48 rms-change max change #iterations 3.745234 165.8925 at 10iterations 1.584794 72.75310 at 20iterations 0.6733403 22.56460 at 30iterations 0.2856657 8.922351 at 40iterations 0.1216415 3.981979 at 50iterations 5.1662754E-02 1.738575 at 60iterations 2.2014648E-02 0.7228241 at 70iterations 9.3695940E-03 0.3090706 at 80iterations 4.0447875E-03 0.1538849 at 90iterations 1.7620928E-03 5.9164762E-02 at 100iterations 7.9564226E-04 3.0268550E-02 at 110iterations 3.7936718E-04 1.4506340E-02 at 120iterations finished qdiffx linear iterations at : 07:50:58 total time elapsed so far: 10.76000 # loops : 120 mean,max change (kT/e) : 3.7936718E-04 1.4506340E-02 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.94000 DelPhi exited at 07:50:59 10.943u 0.443s 0:12.31 92.4% 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 Tue Oct 11 2011 at 07:50:59 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 = 3751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.439395 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): 88.29400 140.0550 ymin,ymax (A): 115.6140 181.2860 zmin,zma (A): -34.23900 23.36400 x,y,z range (A): 51.76099 65.67201 57.60300 scale (grids/A): 2.439395 object centre (A): 114.1745 148.4500 -5.437501 number of atom coordinates read : 3751 total number of charged atoms : 3604 net assigned charge : 9.500016 assigned positive charge : 572.7215 centred at (gu) : 89.97523 88.52615 92.88985 assigned negative charge : -563.2240 centred at (gu) : 89.86298 88.41430 92.86925 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 182681 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35819 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 89469 mr = 127167 m= 29034 mr = 70753 m= 5351 mr = 22171 m= 369 mr = 3548 m= 3 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 83105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 28801 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) : 1.626263 object centre at (A) : 114.1745 148.4500 -5.437501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0251797E-02 0.1621842 midg,1,midg; midg,igrid,midg -0.3571113 0.4230036 1,midg,midg; igrid,midg,midg -1.8435864E-02 7.0298441E-02 gauss-seidel spectral radius is 0.9991922 estimated iterations to convergence 278 setup time was (sec) 2.040000 now iterating at: 07:51:02 rms-change max change #iterations 9.899838 319.0159 at 10iterations 5.730012 148.3360 at 20iterations 3.293387 74.56860 at 30iterations 1.880774 46.77132 at 40iterations 1.071501 24.06388 at 50iterations 0.6088512 11.58312 at 60iterations 0.3456278 7.908045 at 70iterations 0.1953118 4.420722 at 80iterations 0.1100809 2.397118 at 90iterations 6.2224012E-02 1.332413 at 100iterations 3.5017338E-02 0.7075729 at 110iterations 1.9711884E-02 0.4029360 at 120iterations 1.1138605E-02 0.2050686 at 130iterations 6.3159382E-03 0.1237965 at 140iterations 3.5896725E-03 6.7680359E-02 at 150iterations 2.0657757E-03 4.2831421E-02 at 160iterations 1.2096618E-03 2.4721026E-02 at 170iterations 7.2700402E-04 1.4717579E-02 at 180iterations finished qdiffx linear iterations at : 07:51:19 total time elapsed so far: 18.95000 # loops : 180 mean,max change (kT/e) : 7.2700402E-04 1.4717579E-02 energy calculations done at 18.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.13000 DelPhi exited at 07:51:20 19.139u 0.454s 0:20.05 97.6% 0+0k 0+0io 0pf+0w