Tue Oct 11 08:03:10 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 08:03:10 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 = 2650 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5550791 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): 42.57000 83.67700 ymin,ymax (A): 13.21700 73.66200 zmin,zma (A): -21.88300 42.25200 x,y,z range (A): 41.10700 60.44500 64.13500 scale (grids/A): 0.5550791 object centre (A): 63.12350 43.43950 10.18450 number of atom coordinates read : 2650 total number of charged atoms : 2508 net assigned charge : 8.000020 assigned positive charge : 392.2885 centred at (gu) : 90.43588 89.76700 91.92900 assigned negative charge : -384.2895 centred at (gu) : 90.48012 89.63950 91.80443 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5373 nv = 96 ne = 84 npr = 52152 no. pairs analyzed = 52152 no. exposed pairs = 3528 no. arc points = 25257 no. surface atoms = 1197 nbur = 1453 mkacc time = 0.1200000 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 = 1.540000 m= 193 mr = 2592 m= 0 mr = 5 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2591 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6938 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9140897E-10 2.6825953E-09 midg,1,midg; midg,igrid,midg -3.7029632E-10 1.5988433E-09 1,midg,midg; igrid,midg,midg 9.3703090E-10 3.6670622E-10 gauss-seidel spectral radius is 0.9832425 estimated iterations to convergence 64 setup time was (sec) 0.5200000 now iterating at: 08:03:11 rms-change max change #iterations 7.1704447E-02 14.91286 at 10iterations 4.9202996E-03 0.9405723 at 20iterations 3.4226611E-04 7.9725266E-02 at 30iterations 2.3493145E-05 4.3792725E-03 at 40iterations 1.6758568E-06 3.1852722E-04 at 50iterations finished qdiffx linear iterations at : 08:03:13 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.6758568E-06 3.1852722E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 08:03:14 3.169u 0.148s 0:03.60 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 08:03:14 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 = 2650 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.665237 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): 42.57000 83.67700 ymin,ymax (A): 13.21700 73.66200 zmin,zma (A): -21.88300 42.25200 x,y,z range (A): 41.10700 60.44500 64.13500 scale (grids/A): 1.665237 object centre (A): 63.12350 43.43950 10.18450 number of atom coordinates read : 2650 total number of charged atoms : 2508 net assigned charge : 8.000020 assigned positive charge : 392.2885 centred at (gu) : 91.30679 89.29995 95.78614 assigned negative charge : -384.2895 centred at (gu) : 91.44011 88.91826 95.41312 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 59009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25257 grid for indexing accessible points = 1.400000 m= 17278 mr = 38272 m= 1769 mr = 11600 m= 55 mr = 827 m= 0 mr = 8 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 326 time to turn everything in is 0.4500000 number of dielectric boundary points 27404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 19312 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) : 0.5550791 object centre at (A) : 63.12350 43.43950 10.18450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8438055E-04 6.4759187E-02 midg,1,midg; midg,igrid,midg -1.3315199E-02 7.8166453E-03 1,midg,midg; igrid,midg,midg 9.0608746E-03 3.3519107E-03 gauss-seidel spectral radius is 0.9982275 estimated iterations to convergence 189 setup time was (sec) 0.7200000 now iterating at: 08:03:15 rms-change max change #iterations 3.170415 158.7339 at 10iterations 1.325382 52.69203 at 20iterations 0.5565860 20.81252 at 30iterations 0.2336953 9.545038 at 40iterations 9.8311789E-02 3.536064 at 50iterations 4.1307230E-02 1.582243 at 60iterations 1.7376499E-02 0.6496811 at 70iterations 7.3243766E-03 0.2812691 at 80iterations 3.0837357E-03 0.1226101 at 90iterations 1.3007442E-03 4.6995640E-02 at 100iterations 5.4511166E-04 1.9271851E-02 at 110iterations 2.2947474E-04 8.2273483E-03 at 120iterations finished qdiffx linear iterations at : 08:03:21 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 2.2947474E-04 8.2273483E-03 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 08:03:21 7.105u 0.216s 0:07.79 93.8% 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 Tue Oct 11 2011 at 08:03:22 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 = 2650 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.497856 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): 42.57000 83.67700 ymin,ymax (A): 13.21700 73.66200 zmin,zma (A): -21.88300 42.25200 x,y,z range (A): 41.10700 60.44500 64.13500 scale (grids/A): 2.497856 object centre (A): 63.12350 43.43950 10.18450 number of atom coordinates read : 2650 total number of charged atoms : 2508 net assigned charge : 8.000020 assigned positive charge : 392.2885 centred at (gu) : 91.96012 88.94995 98.67903 assigned negative charge : -384.2895 centred at (gu) : 92.16016 88.37727 98.11965 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 136898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25257 grid for indexing accessible points = 1.400000 m= 60138 mr = 93966 m= 16714 mr = 46721 m= 2643 mr = 12358 m= 203 mr = 1687 m= 9 mr = 98 m= 0 mr = 3 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1181 time to turn everything in is 0.9800000 number of dielectric boundary points 61772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 20041 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) : 1.665237 object centre at (A) : 63.12350 43.43950 10.18450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8348654E-02 1.292559 midg,1,midg; midg,igrid,midg -0.2663828 6.4907402E-02 1,midg,midg; igrid,midg,midg 0.1222828 3.6951639E-02 gauss-seidel spectral radius is 0.9991441 estimated iterations to convergence 270 setup time was (sec) 1.280000 now iterating at: 08:03:23 rms-change max change #iterations 8.219298 350.9196 at 10iterations 4.598456 131.2182 at 20iterations 2.571022 62.67962 at 30iterations 1.428892 33.40522 at 40iterations 0.7930531 17.75773 at 50iterations 0.4375220 10.55092 at 60iterations 0.2420196 5.517886 at 70iterations 0.1333352 2.949753 at 80iterations 7.3557988E-02 1.492138 at 90iterations 4.0526319E-02 0.8748627 at 100iterations 2.2332605E-02 0.5602798 at 110iterations 1.2297841E-02 0.2669749 at 120iterations 6.7516421E-03 0.1375198 at 130iterations 3.7025225E-03 8.1392288E-02 at 140iterations 2.0381496E-03 4.1511536E-02 at 150iterations 1.1216929E-03 2.3480415E-02 at 160iterations 6.1624474E-04 1.2840271E-02 at 170iterations 3.3860782E-04 7.0610046E-03 at 180iterations finished qdiffx linear iterations at : 08:03:33 total time elapsed so far: 11.11000 # loops : 180 mean,max change (kT/e) : 3.3860782E-04 7.0610046E-03 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 08:03:33 11.288u 0.202s 0:11.78 97.4% 0+0k 0+0io 0pf+0w