Tue Oct 11 03:28:45 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+sph2.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 = amb2.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 03:28:45 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 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: 0.6215518 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): -14.48600 42.79000 ymin,ymax (A): -0.8990000 54.99000 zmin,zma (A): 32.81100 90.03699 x,y,z range (A): 57.27600 55.88900 57.22599 scale (grids/A): 0.6215518 object centre (A): 14.15200 27.04550 61.42400 number of atom coordinates read : 3077 total number of charged atoms : 2922 net assigned charge : 0.5000052 assigned positive charge : 465.1952 centred at (gu) : 90.34578 90.03151 90.75677 assigned negative charge : -464.6962 centred at (gu) : 90.43600 90.14392 90.55591 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8171 nv = 96 ne = 84 npr = 59754 no. pairs analyzed = 59754 no. exposed pairs = 4337 no. arc points = 30064 no. surface atoms = 1441 nbur = 1636 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 4139 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2200000 number of dielectric boundary points 4415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2980 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9832 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4155890E-08 1.9786318E-08 midg,1,midg; midg,igrid,midg 9.5154089E-09 -9.2035615E-09 1,midg,midg; igrid,midg,midg 7.1999144E-09 -7.8366122E-09 gauss-seidel spectral radius is 0.9866477 estimated iterations to convergence 71 setup time was (sec) 0.4200000 now iterating at: 03:28:46 rms-change max change #iterations 0.1392236 21.42234 at 10iterations 1.3005784E-02 1.979816 at 20iterations 1.1876517E-03 0.1861877 at 30iterations 1.1142175E-04 1.8714905E-02 at 40iterations 1.1005462E-05 1.5068054E-03 at 50iterations finished qdiffx linear iterations at : 03:28:49 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.1005462E-05 1.5068054E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 03:28:49 3.365u 0.156s 0:03.83 91.6% 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 03:28:49 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 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: 1.864655 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): -14.48600 42.79000 ymin,ymax (A): -0.8990000 54.99000 zmin,zma (A): 32.81100 90.03699 x,y,z range (A): 57.27600 55.88900 57.22599 scale (grids/A): 1.864655 object centre (A): 14.15200 27.04550 61.42400 number of atom coordinates read : 3077 total number of charged atoms : 2922 net assigned charge : 0.5000052 assigned positive charge : 465.1952 centred at (gu) : 91.03632 90.09399 92.26960 assigned negative charge : -464.6962 centred at (gu) : 91.30759 90.43130 91.66747 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 87773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30064 grid for indexing accessible points = 1.400000 m= 29896 mr = 58339 m= 4137 mr = 20628 m= 246 mr = 2270 m= 5 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 756 time to turn everything in is 0.4200000 number of dielectric boundary points 40758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 22971 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) : 0.6215518 object centre at (A) : 14.15200 27.04550 61.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5640755E-02 2.1229779E-02 midg,1,midg; midg,igrid,midg 2.3640979E-02 1.5077458E-03 1,midg,midg; igrid,midg,midg 2.2784304E-02 -1.5072861E-02 gauss-seidel spectral radius is 0.9986392 estimated iterations to convergence 215 setup time was (sec) 0.6200000 now iterating at: 03:28:50 rms-change max change #iterations 4.485639 166.8823 at 10iterations 2.106076 70.13573 at 20iterations 0.9801619 31.50858 at 30iterations 0.4592250 14.94484 at 40iterations 0.2150698 6.806541 at 50iterations 0.1004893 3.065148 at 60iterations 4.6973344E-02 1.464016 at 70iterations 2.2001337E-02 0.6543949 at 80iterations 1.0309641E-02 0.3268318 at 90iterations 4.8334138E-03 0.1459436 at 100iterations 2.2616177E-03 6.5406799E-02 at 110iterations 1.0588220E-03 3.4957886E-02 at 120iterations finished qdiffx linear iterations at : 03:28:57 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.0588220E-03 3.4957886E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 03:28:57 7.786u 0.200s 0:08.27 96.4% 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 03:28:57 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 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: 2.796983 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): -14.48600 42.79000 ymin,ymax (A): -0.8990000 54.99000 zmin,zma (A): 32.81100 90.03699 x,y,z range (A): 57.27600 55.88900 57.22599 scale (grids/A): 2.796983 object centre (A): 14.15200 27.04550 61.42400 number of atom coordinates read : 3077 total number of charged atoms : 2922 net assigned charge : 0.5000052 assigned positive charge : 465.1952 centred at (gu) : 91.55441 90.14093 93.40427 assigned negative charge : -464.6962 centred at (gu) : 91.96131 90.64698 92.50121 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 202723 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30064 grid for indexing accessible points = 1.400000 m= 98220 mr = 142377 m= 32505 mr = 77288 m= 7029 mr = 24597 m= 968 mr = 4829 m= 42 mr = 548 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 2955 time to turn everything in is 1.080000 number of dielectric boundary points 91839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 23373 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) : 1.864655 object centre at (A) : 14.15200 27.04550 61.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9256533 0.1205458 midg,1,midg; midg,igrid,midg 0.2348582 9.1118097E-02 1,midg,midg; igrid,midg,midg 0.2836944 -0.1863870 gauss-seidel spectral radius is 0.9992839 estimated iterations to convergence 295 setup time was (sec) 1.320000 now iterating at: 03:28:59 rms-change max change #iterations 10.86444 330.5304 at 10iterations 6.501867 144.5220 at 20iterations 3.854239 86.10118 at 30iterations 2.261654 48.49763 at 40iterations 1.329693 28.10125 at 50iterations 0.7797214 13.89845 at 60iterations 0.4548073 8.877423 at 70iterations 0.2647785 4.721960 at 80iterations 0.1544011 2.952533 at 90iterations 8.9821264E-02 1.820393 at 100iterations 5.2225936E-02 1.171708 at 110iterations 3.0354386E-02 0.5340157 at 120iterations 1.7659485E-02 0.3420763 at 130iterations 1.0220089E-02 0.1986427 at 140iterations 5.9481314E-03 0.1062069 at 150iterations 3.4472188E-03 6.0375214E-02 at 160iterations 2.0011158E-03 3.4362793E-02 at 170iterations 1.1636147E-03 1.9372940E-02 at 180iterations finished qdiffx linear iterations at : 03:29:11 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 1.1636147E-03 1.9372940E-02 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 03:29:11 13.069u 0.196s 0:13.66 96.9% 0+0k 0+0io 0pf+0w