Tue Oct 11 06:22:11 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 06:22:11 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 = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7070787 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): 3.274000 47.94900 ymin,ymax (A): -13.22100 28.49900 zmin,zma (A): -13.71500 36.63300 x,y,z range (A): 44.67500 41.72000 50.34800 scale (grids/A): 0.7070787 object centre (A): 25.61150 7.639000 11.45900 number of atom coordinates read : 2004 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.61279 90.08744 89.49876 assigned negative charge : -304.2972 centred at (gu) : 89.78262 90.10277 89.46317 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6867 nv = 96 ne = 84 npr = 39138 no. pairs analyzed = 39138 no. exposed pairs = 2446 no. arc points = 16808 no. surface atoms = 840 nbur = 1164 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 3958 m= 3 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1591 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7724 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9866561E-08 7.2313235E-08 midg,1,midg; midg,igrid,midg 6.8741457E-08 5.6126911E-08 1,midg,midg; igrid,midg,midg 1.5363528E-07 -1.8323918E-08 gauss-seidel spectral radius is 0.9895674 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 06:22:12 rms-change max change #iterations 0.1952320 30.39041 at 10iterations 2.4766101E-02 3.647663 at 20iterations 3.1866946E-03 0.4556293 at 30iterations 4.9601833E-04 6.9704533E-02 at 40iterations 1.1198661E-04 1.5926361E-02 at 50iterations finished qdiffx linear iterations at : 06:22:14 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.1198661E-04 1.5926361E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:22:15 3.328u 0.170s 0:04.03 86.6% 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 06:22:15 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 = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.121236 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): 3.274000 47.94900 ymin,ymax (A): -13.22100 28.49900 zmin,zma (A): -13.71500 36.63300 x,y,z range (A): 44.67500 41.72000 50.34800 scale (grids/A): 2.121236 object centre (A): 25.61150 7.639000 11.45900 number of atom coordinates read : 2004 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 88.83842 90.26224 88.49621 assigned negative charge : -304.2972 centred at (gu) : 89.34787 90.30843 88.38947 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 72818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16808 grid for indexing accessible points = 1.400000 m= 29129 mr = 51766 m= 5737 mr = 22073 m= 511 mr = 3776 m= 10 mr = 253 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 30335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15335 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) : 0.7070787 object centre at (A) : 25.61150 7.639000 11.45900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1873019E-02 4.6755377E-02 midg,1,midg; midg,igrid,midg 2.5130525E-02 4.8879306E-03 1,midg,midg; igrid,midg,midg 4.7052473E-02 1.4708398E-02 gauss-seidel spectral radius is 0.9988241 estimated iterations to convergence 231 setup time was (sec) 0.5700000 now iterating at: 06:22:16 rms-change max change #iterations 4.520655 190.0610 at 10iterations 2.230726 74.44826 at 20iterations 1.106124 33.85776 at 30iterations 0.5474703 15.59082 at 40iterations 0.2715237 8.635643 at 50iterations 0.1347360 4.032597 at 60iterations 6.6722155E-02 2.081244 at 70iterations 3.3220559E-02 1.000871 at 80iterations 1.6541796E-02 0.4708833 at 90iterations 8.2539031E-03 0.2517090 at 100iterations 4.1502216E-03 0.1241007 at 110iterations 2.1245540E-03 6.7879498E-02 at 120iterations finished qdiffx linear iterations at : 06:22:23 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 2.1245540E-03 6.7879498E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 06:22:24 7.638u 0.195s 0:08.40 93.0% 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 06:22:24 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 = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.181854 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): 3.274000 47.94900 ymin,ymax (A): -13.22100 28.49900 zmin,zma (A): -13.71500 36.63300 x,y,z range (A): 44.67500 41.72000 50.34800 scale (grids/A): 3.181854 object centre (A): 25.61150 7.639000 11.45900 number of atom coordinates read : 2004 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 88.25765 90.39329 87.74434 assigned negative charge : -304.2972 centred at (gu) : 89.02180 90.46270 87.58418 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 167975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16808 grid for indexing accessible points = 1.400000 m= 91153 mr = 124664 m= 36777 mr = 75754 m= 10749 mr = 30239 m= 2118 mr = 8272 m= 233 mr = 1533 m= 7 mr = 158 m= 0 mr = 5 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 68387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 15432 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) : 2.121236 object centre at (A) : 25.61150 7.639000 11.45900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6223655 0.3494021 midg,1,midg; midg,igrid,midg 0.2002590 -1.1565784E-02 1,midg,midg; igrid,midg,midg 0.3529586 0.2146734 gauss-seidel spectral radius is 0.9992907 estimated iterations to convergence 296 setup time was (sec) 1.340000 now iterating at: 06:22:25 rms-change max change #iterations 10.09369 308.0695 at 10iterations 5.968962 130.8011 at 20iterations 3.518296 70.70753 at 30iterations 2.077520 42.48037 at 40iterations 1.219492 28.12459 at 50iterations 0.7174639 14.52852 at 60iterations 0.4194094 8.011192 at 70iterations 0.2457347 4.871382 at 80iterations 0.1441991 2.645693 at 90iterations 8.4295273E-02 1.598389 at 100iterations 4.9512658E-02 0.8773193 at 110iterations 2.9212922E-02 0.5121651 at 120iterations 1.7311759E-02 0.3238869 at 130iterations 1.0436619E-02 0.2019062 at 140iterations 6.4446665E-03 0.1136818 at 150iterations 4.1453918E-03 7.9505920E-02 at 160iterations 2.8301321E-03 5.1284790E-02 at 170iterations 2.0437425E-03 3.8682938E-02 at 180iterations finished qdiffx linear iterations at : 06:22:36 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 2.0437425E-03 3.8682938E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 06:22:37 12.531u 0.201s 0:13.04 97.6% 0+0k 0+0io 0pf+0w