Mon Oct 10 17:14:00 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 17:14:01 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: 249 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: 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 : 1.700005 assigned positive charge : 421.1314 centred at (gu) : 87.56736 90.81535 90.21922 assigned negative charge : -419.4324 centred at (gu) : 87.70338 90.76914 90.20302 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 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 = 0.1000000 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 = 0.1100000 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 -6.0744625E-11 1.0213210E-09 midg,1,midg; midg,igrid,midg -8.4981333E-10 2.3242228E-09 1,midg,midg; igrid,midg,midg 8.4032425E-09 -2.2571525E-09 gauss-seidel spectral radius is 0.9853281 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 17:14:01 rms-change max change #iterations 0.1057843 18.27385 at 10iterations 8.8504599E-03 1.423065 at 20iterations 7.8499585E-04 0.1144161 at 30iterations 8.7837740E-05 1.5137672E-02 at 40iterations 1.5263360E-05 2.1553040E-03 at 50iterations finished qdiffx linear iterations at : 17:14:04 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.5263360E-05 2.1553040E-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) 3.470000 DelPhi exited at 17:14:05 3.474u 0.183s 0:04.63 78.8% 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 17:14:05 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: 249 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 : 1.700005 assigned positive charge : 421.1314 centred at (gu) : 82.70177 92.44534 90.65726 assigned negative charge : -419.4324 centred at (gu) : 83.10960 92.30714 90.60906 start vw surface at 9.0000004E-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 0.3600000 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 0.4400000 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 7.0267334E-04 2.7290233E-03 midg,1,midg; midg,igrid,midg 5.7815653E-03 2.8152166E-02 1,midg,midg; igrid,midg,midg 2.9321134E-02 -1.7664088E-02 gauss-seidel spectral radius is 0.9984592 estimated iterations to convergence 202 setup time was (sec) 0.5800000 now iterating at: 17:14:06 rms-change max change #iterations 3.866395 151.7279 at 10iterations 1.731525 58.14552 at 20iterations 0.7703470 26.25088 at 30iterations 0.3446270 12.71924 at 40iterations 0.1547200 5.298896 at 50iterations 6.9193386E-02 2.472445 at 60iterations 3.0980159E-02 0.9953917 at 70iterations 1.3825038E-02 0.4551392 at 80iterations 6.2111863E-03 0.2003756 at 90iterations 2.7766731E-03 9.2184067E-02 at 100iterations 1.2457179E-03 3.9031982E-02 at 110iterations 5.6091731E-04 1.7379761E-02 at 120iterations finished qdiffx linear iterations at : 17:14:13 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 5.6091731E-04 1.7379761E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 17:14:14 7.929u 0.201s 0:08.86 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 Mon Oct 10 2011 at 17:14:14 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: 249 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: 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 : 1.700005 assigned positive charge : 421.1314 centred at (gu) : 79.05240 93.66779 90.98575 assigned negative charge : -419.4324 centred at (gu) : 79.66434 93.46078 90.91337 start vw surface at 7.9999998E-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 = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 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 0.9600000 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 5.9119649E-02 6.4870574E-02 midg,1,midg; midg,igrid,midg 1.9281624E-02 0.4114622 1,midg,midg; igrid,midg,midg 0.6068695 -0.2751456 gauss-seidel spectral radius is 0.9992163 estimated iterations to convergence 282 setup time was (sec) 1.100000 now iterating at: 17:14:15 rms-change max change #iterations 9.508926 308.5912 at 10iterations 5.500937 148.0062 at 20iterations 3.178541 80.32755 at 30iterations 1.817538 35.88863 at 40iterations 1.039925 24.29143 at 50iterations 0.5922800 12.96614 at 60iterations 0.3368869 7.227724 at 70iterations 0.1915104 3.917085 at 80iterations 0.1088633 2.155400 at 90iterations 6.1837818E-02 1.150946 at 100iterations 3.5038706E-02 0.6852283 at 110iterations 1.9824235E-02 0.3925557 at 120iterations 1.1224322E-02 0.2210217 at 130iterations 6.3531003E-03 0.1233635 at 140iterations 3.6023718E-03 7.1540833E-02 at 150iterations 2.0330460E-03 4.1839600E-02 at 160iterations 1.1558386E-03 2.1770716E-02 at 170iterations 6.5492914E-04 1.2264252E-02 at 180iterations finished qdiffx linear iterations at : 17:14:27 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 6.5492914E-04 1.2264252E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 17:14:28 12.723u 0.242s 0:13.47 96.2% 0+0k 0+0io 0pf+0w