Mon Oct 10 11:06:39 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 11:06:39 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 = 5402 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4877781 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 0.4877781 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 853.1913 centred at (gu) : 89.32305 90.44461 88.24685 assigned negative charge : -841.2001 centred at (gu) : 89.29803 90.49448 88.22227 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8120 nv = 96 ne = 84 npr = 106473 no. pairs analyzed = 106473 no. exposed pairs = 6506 no. arc points = 44171 no. surface atoms = 2193 nbur = 3209 mkacc time = 0.2500000 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 = 1.736000 m= 252 mr = 4337 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4292 ## 679 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 10892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1193411E-11 5.3885504E-11 midg,1,midg; midg,igrid,midg 1.0071523E-10 4.6765898E-12 1,midg,midg; igrid,midg,midg 3.8054296E-11 7.2244405E-11 gauss-seidel spectral radius is 0.9785555 estimated iterations to convergence 57 setup time was (sec) 0.7900000 now iterating at: 11:06:40 rms-change max change #iterations 5.6938466E-02 9.472595 at 10iterations 3.2086819E-03 0.5461197 at 20iterations 7.6108321E-04 0.1204777 at 30iterations 3.7162288E-04 5.9527397E-02 at 40iterations 1.8638125E-04 3.0097485E-02 at 50iterations finished qdiffx linear iterations at : 11:06:43 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 1.8638125E-04 3.0097485E-02 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.860000 DelPhi exited at 11:06:44 3.860u 0.198s 0:04.33 93.5% 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 Mon Oct 10 2011 at 11:06:44 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 = 5402 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: 1.463334 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 1.463334 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 853.1913 centred at (gu) : 87.96747 91.33187 84.73854 assigned negative charge : -841.2001 centred at (gu) : 87.89391 91.48364 84.66673 start vw surface at 0.2400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 93556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44171 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 26239 mr = 66234 m= 1951 mr = 17503 m= 37 mr = 742 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1970 time to turn everything in is 0.7100000 number of dielectric boundary points 37304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 703 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 38804 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) : 0.4877781 object centre at (A) : -11.71000 5.882999 41.22550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8188580E-04 3.4197909E-03 midg,1,midg; midg,igrid,midg 8.6037740E-03 -2.4688531E-02 1,midg,midg; igrid,midg,midg 9.5268380E-04 1.5008350E-02 gauss-seidel spectral radius is 0.9979509 estimated iterations to convergence 176 setup time was (sec) 1.030000 now iterating at: 11:06:45 rms-change max change #iterations 3.730757 142.6780 at 10iterations 1.473791 48.68752 at 20iterations 0.5829352 21.14723 at 30iterations 0.2310964 7.275362 at 40iterations 9.1262385E-02 2.714890 at 50iterations 3.6185384E-02 1.197777 at 60iterations 1.4458919E-02 0.4756813 at 70iterations 5.8804099E-03 0.2015572 at 80iterations 2.5263606E-03 8.9780331E-02 at 90iterations 1.2639471E-03 4.8328400E-02 at 100iterations 7.8933832E-04 2.8982162E-02 at 110iterations 5.6863774E-04 2.0851135E-02 at 120iterations finished qdiffx linear iterations at : 11:06:52 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 5.6863774E-04 2.0851135E-02 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 11:06:53 8.489u 0.238s 0:08.99 96.8% 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 11:06:53 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 = 5402 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: 2.195002 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): -45.68100 22.26100 ymin,ymax (A): -30.60900 42.37500 zmin,zma (A): 10.14500 72.30600 x,y,z range (A): 67.94200 72.98400 62.16100 scale (grids/A): 2.195002 object centre (A): -11.71000 5.882999 41.22550 number of atom coordinates read : 5402 total number of charged atoms : 5247 net assigned charge : 12.00002 assigned positive charge : 853.1913 centred at (gu) : 86.95088 91.99732 82.10742 assigned negative charge : -841.2001 centred at (gu) : 86.84084 92.22561 82.00021 start vw surface at 0.2300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 218754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44171 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 97028 mr = 162687 m= 22385 mr = 76535 m= 2554 mr = 15890 m= 104 mr = 1466 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 6578 time to turn everything in is 1.620000 number of dielectric boundary points 84228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 41765 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) : 1.463334 object centre at (A) : -11.71000 5.882999 41.22550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8810081E-02 5.3849392E-02 midg,1,midg; midg,igrid,midg 0.1657842 -0.8141429 1,midg,midg; igrid,midg,midg -2.8247425E-02 0.2653686 gauss-seidel spectral radius is 0.9991143 estimated iterations to convergence 265 setup time was (sec) 1.930000 now iterating at: 11:06:55 rms-change max change #iterations 10.33213 315.3264 at 10iterations 5.783573 149.7121 at 20iterations 3.216250 93.72562 at 30iterations 1.783159 48.49327 at 40iterations 0.9834683 22.77491 at 50iterations 0.5415980 10.67000 at 60iterations 0.2974558 6.302958 at 70iterations 0.1631109 3.180252 at 80iterations 8.9288533E-02 1.762845 at 90iterations 4.8894137E-02 0.9126911 at 100iterations 2.6788443E-02 0.4848366 at 110iterations 1.4653650E-02 0.2670670 at 120iterations 8.0147982E-03 0.1450748 at 130iterations 4.4037169E-03 8.4312439E-02 at 140iterations 2.4242536E-03 5.2660942E-02 at 150iterations 1.3637411E-03 2.6050568E-02 at 160iterations 7.9029857E-04 1.6059875E-02 at 170iterations 4.8602474E-04 1.0599136E-02 at 180iterations finished qdiffx linear iterations at : 11:07:05 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 4.8602474E-04 1.0599136E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 11:07:06 12.629u 0.199s 0:13.13 97.5% 0+0k 0+0io 0pf+0w