Mon Oct 10 17:14:28 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 Mon Oct 10 2011 at 17:14:28 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2808 !!! WARNING: HIZ 82 has a net charge of 0.2000 !!! WARNING: HIZ 118 has a net charge of 0.2000 !!! WARNING: GLU 324 has a net charge of -2.0000 !!! WARNING: MG3 326 has a net charge of 1.4000 !!! WARNING: ZN3 327 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5935509 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): -13.76800 46.21000 ymin,ymax (A): -30.75900 23.49900 zmin,zma (A): -7.049000 41.16900 x,y,z range (A): 59.97800 54.25800 48.21800 scale (grids/A): 0.5935509 object centre (A): 16.22100 -3.629999 17.06000 number of atom coordinates read : 2808 total number of charged atoms : 2665 net assigned charge : 1.700006 assigned positive charge : 423.9315 centred at (gu) : 87.58013 90.80289 90.17502 assigned negative charge : -422.2324 centred at (gu) : 87.71709 90.75384 90.16277 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6453 nv = 96 ne = 84 npr = 58222 no. pairs analyzed = 58222 no. exposed pairs = 3412 no. arc points = 23891 no. surface atoms = 1160 nbur = 1648 mkacc time = 9.9999994E-02 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 = 1.456000 m= 298 mr = 3480 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2516 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8221 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6643856E-11 8.8158880E-10 midg,1,midg; midg,igrid,midg -9.3848007E-10 2.4379081E-09 1,midg,midg; igrid,midg,midg 8.4795531E-09 -2.2994191E-09 gauss-seidel spectral radius is 0.9853281 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 17:14:28 rms-change max change #iterations 0.1085311 19.52785 at 10iterations 9.0829274E-03 1.518361 at 20iterations 8.1190129E-04 0.1208477 at 30iterations 9.3935167E-05 1.6466141E-02 at 40iterations 1.7001286E-05 2.4213791E-03 at 50iterations finished qdiffx linear iterations at : 17:14:31 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.7001286E-05 2.4213791E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 17:14:32 3.489u 0.177s 0:04.17 87.5% 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 17:14:32 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2808 !!! WARNING: HIZ 82 has a net charge of 0.2000 !!! WARNING: HIZ 118 has a net charge of 0.2000 !!! WARNING: GLU 324 has a net charge of -2.0000 !!! WARNING: MG3 326 has a net charge of 1.4000 !!! WARNING: ZN3 327 has a net charge of 1.4000 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: 1.780653 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): -13.76800 46.21000 ymin,ymax (A): -30.75900 23.49900 zmin,zma (A): -7.049000 41.16900 x,y,z range (A): 59.97800 54.25800 48.21800 scale (grids/A): 1.780653 object centre (A): 16.22100 -3.629999 17.06000 number of atom coordinates read : 2808 total number of charged atoms : 2665 net assigned charge : 1.700006 assigned positive charge : 423.9315 centred at (gu) : 82.74018 92.40806 90.52467 assigned negative charge : -422.2324 centred at (gu) : 83.15073 92.26122 90.48830 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23891 grid for indexing accessible points = 1.400000 m= 23622 mr = 49590 m= 3146 mr = 16791 m= 128 mr = 1749 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 30095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 230 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20796 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) : 0.5935509 object centre at (A) : 16.22100 -3.629999 17.06000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8131828E-03 2.6511797E-03 midg,1,midg; midg,igrid,midg 4.9455492E-03 2.8586539E-02 1,midg,midg; igrid,midg,midg 2.9546432E-02 -1.7808994E-02 gauss-seidel spectral radius is 0.9984592 estimated iterations to convergence 202 setup time was (sec) 0.5600000 now iterating at: 17:14:33 rms-change max change #iterations 3.905625 151.7279 at 10iterations 1.748405 62.12239 at 20iterations 0.7776334 26.25087 at 30iterations 0.3477881 12.85956 at 40iterations 0.1561838 5.408562 at 50iterations 6.9849335E-02 2.426399 at 60iterations 3.1285357E-02 0.9874516 at 70iterations 1.3956750E-02 0.4627285 at 80iterations 6.2704314E-03 0.2005615 at 90iterations 2.8061520E-03 9.5373154E-02 at 100iterations 1.2589393E-03 3.9242744E-02 at 110iterations 5.6767627E-04 1.7599106E-02 at 120iterations finished qdiffx linear iterations at : 17:14:40 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 5.6767627E-04 1.7599106E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 17:14:41 7.911u 0.210s 0:08.48 95.7% 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 17:14:41 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2808 !!! WARNING: HIZ 82 has a net charge of 0.2000 !!! WARNING: HIZ 118 has a net charge of 0.2000 !!! WARNING: GLU 324 has a net charge of -2.0000 !!! WARNING: MG3 326 has a net charge of 1.4000 !!! WARNING: ZN3 327 has a net charge of 1.4000 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: 2.670979 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): -13.76800 46.21000 ymin,ymax (A): -30.75900 23.49900 zmin,zma (A): -7.049000 41.16900 x,y,z range (A): 59.97800 54.25800 48.21800 scale (grids/A): 2.670979 object centre (A): 16.22100 -3.629999 17.06000 number of atom coordinates read : 2808 total number of charged atoms : 2665 net assigned charge : 1.700006 assigned positive charge : 423.9315 centred at (gu) : 79.11002 93.61187 90.78687 assigned negative charge : -422.2324 centred at (gu) : 79.72604 93.39189 90.73225 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 165496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23891 grid for indexing accessible points = 1.400000 m= 78650 mr = 120644 m= 25586 mr = 63184 m= 5287 mr = 19775 m= 566 mr = 3772 m= 17 mr = 320 m= 0 mr = 2 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 67905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 21313 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) : 1.780653 object centre at (A) : 16.22100 -3.629999 17.06000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4335277E-02 6.3940741E-02 midg,1,midg; midg,igrid,midg 7.7653695E-03 0.4169127 1,midg,midg; igrid,midg,midg 0.6090234 -0.2768262 gauss-seidel spectral radius is 0.9992163 estimated iterations to convergence 282 setup time was (sec) 1.120000 now iterating at: 17:14:42 rms-change max change #iterations 9.589061 308.5916 at 10iterations 5.544755 149.0845 at 20iterations 3.203107 79.46060 at 30iterations 1.831396 36.21515 at 40iterations 1.047514 24.29811 at 50iterations 0.5962577 13.40881 at 60iterations 0.3391308 7.171440 at 70iterations 0.1927837 4.009298 at 80iterations 0.1095833 2.190897 at 90iterations 6.2239908E-02 1.155821 at 100iterations 3.5269313E-02 0.6887226 at 110iterations 1.9951416E-02 0.3950119 at 120iterations 1.1294121E-02 0.2197380 at 130iterations 6.3958010E-03 0.1246681 at 140iterations 3.6270504E-03 7.2772026E-02 at 150iterations 2.0472226E-03 4.1011810E-02 at 160iterations 1.1647487E-03 2.2218287E-02 at 170iterations 6.6060643E-04 1.2550354E-02 at 180iterations finished qdiffx linear iterations at : 17:14:53 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 6.6060643E-04 1.2550354E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 17:14:54 12.775u 0.208s 0:13.27 97.7% 0+0k 0+0io 0pf+0w