Mon Oct 10 09:24:49 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 09:24:49 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 0.6095577 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): -9.146000 49.25700 ymin,ymax (A): 8.769000 48.01300 zmin,zma (A): -3.752000 38.62900 x,y,z range (A): 58.40300 39.24400 42.38100 scale (grids/A): 0.6095577 object centre (A): 20.05550 28.39100 17.43850 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 288.6041 centred at (gu) : 90.08394 89.65559 90.52136 assigned negative charge : -283.6043 centred at (gu) : 90.06860 89.56479 90.62416 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4889 nv = 96 ne = 84 npr = 40078 no. pairs analyzed = 40078 no. exposed pairs = 2468 no. arc points = 17463 no. surface atoms = 838 nbur = 1130 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 233 mr = 2668 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1812 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6000 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8557861E-09 -8.8216695E-10 midg,1,midg; midg,igrid,midg -3.6660691E-10 5.7024896E-09 1,midg,midg; igrid,midg,midg 2.3569209E-09 3.5589141E-09 gauss-seidel spectral radius is 0.9860139 estimated iterations to convergence 69 setup time was (sec) 0.5200000 now iterating at: 09:24:50 rms-change max change #iterations 0.1003129 18.84382 at 10iterations 8.7291291E-03 1.577133 at 20iterations 7.5599126E-04 0.1447754 at 30iterations 6.7277928E-05 1.2378693E-02 at 40iterations 5.8833130E-06 1.0321140E-03 at 50iterations finished qdiffx linear iterations at : 09:24:54 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 5.8833130E-06 1.0321140E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.600000 DelPhi exited at 09:24:55 4.609u 0.413s 0:05.43 92.2% 0+0k 0+0io 6pf+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 09:24:55 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 1.828673 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): -9.146000 49.25700 ymin,ymax (A): 8.769000 48.01300 zmin,zma (A): -3.752000 38.62900 x,y,z range (A): 58.40300 39.24400 42.38100 scale (grids/A): 1.828673 object centre (A): 20.05550 28.39100 17.43850 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 288.6041 centred at (gu) : 90.25199 88.96681 91.56423 assigned negative charge : -283.6043 centred at (gu) : 90.20609 88.69440 91.87253 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 53478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17463 grid for indexing accessible points = 1.400000 m= 18060 mr = 36425 m= 2250 mr = 13488 m= 62 mr = 1338 m= 0 mr = 13 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 2478 time to turn everything in is 0.4300000 number of dielectric boundary points 22586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14411 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) : 0.6095577 object centre at (A) : 20.05550 28.39100 17.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0208174E-02 -1.3951095E-03 midg,1,midg; midg,igrid,midg 1.5982080E-03 6.6968556E-03 1,midg,midg; igrid,midg,midg 3.6668841E-02 3.0420210E-02 gauss-seidel spectral radius is 0.9984469 estimated iterations to convergence 201 setup time was (sec) 0.7000000 now iterating at: 09:24:56 rms-change max change #iterations 3.272830 157.3723 at 10iterations 1.451388 61.02862 at 20iterations 0.6483955 25.68428 at 30iterations 0.2873217 11.62696 at 40iterations 0.1284233 4.515580 at 50iterations 5.7147149E-02 2.208461 at 60iterations 2.5432812E-02 0.9266329 at 70iterations 1.1285124E-02 0.4600372 at 80iterations 5.0297072E-03 0.1885052 at 90iterations 2.2426064E-03 9.5113039E-02 at 100iterations 9.9120499E-04 3.7338257E-02 at 110iterations 4.4603893E-04 1.7209530E-02 at 120iterations finished qdiffx linear iterations at : 09:25:05 total time elapsed so far: 10.26000 # loops : 120 mean,max change (kT/e) : 4.4603893E-04 1.7209530E-02 energy calculations done at 10.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.43000 DelPhi exited at 09:25:06 10.433u 0.450s 0:11.13 97.7% 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 09:25:06 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 2.743010 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): -9.146000 49.25700 ymin,ymax (A): 8.769000 48.01300 zmin,zma (A): -3.752000 38.62900 x,y,z range (A): 58.40300 39.24400 42.38100 scale (grids/A): 2.743010 object centre (A): 20.05550 28.39100 17.43850 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 288.6041 centred at (gu) : 90.37795 88.45031 92.34639 assigned negative charge : -283.6043 centred at (gu) : 90.30904 88.04158 92.80886 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 123454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17463 grid for indexing accessible points = 1.400000 m= 60191 mr = 88047 m= 19942 mr = 49463 m= 3810 mr = 16199 m= 308 mr = 2875 m= 11 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 8302 time to turn everything in is 1.090000 number of dielectric boundary points 50951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 14686 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) : 1.828673 object centre at (A) : 20.05550 28.39100 17.43850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7475114E-02 6.8315379E-03 midg,1,midg; midg,igrid,midg 3.9532050E-02 4.9068224E-02 1,midg,midg; igrid,midg,midg 0.4847375 0.3143822 gauss-seidel spectral radius is 0.9991898 estimated iterations to convergence 277 setup time was (sec) 1.390000 now iterating at: 09:25:08 rms-change max change #iterations 7.874915 433.7288 at 10iterations 4.452082 136.0626 at 20iterations 2.506651 68.22760 at 30iterations 1.399717 32.84823 at 40iterations 0.7861641 19.10183 at 50iterations 0.4386096 9.681530 at 60iterations 0.2445440 5.462233 at 70iterations 0.1367852 2.895790 at 80iterations 7.6393411E-02 1.632554 at 90iterations 4.2636607E-02 0.9569130 at 100iterations 2.3786480E-02 0.5139487 at 110iterations 1.3296659E-02 0.2776890 at 120iterations 7.4067237E-03 0.1720667 at 130iterations 4.1570859E-03 0.1046696 at 140iterations 2.3177241E-03 4.8889160E-02 at 150iterations 1.2914621E-03 2.6084900E-02 at 160iterations 7.2120212E-04 1.5029907E-02 at 170iterations 4.0432546E-04 8.6569786E-03 at 180iterations finished qdiffx linear iterations at : 09:25:23 total time elapsed so far: 16.53000 # loops : 180 mean,max change (kT/e) : 4.0432546E-04 8.6569786E-03 energy calculations done at 16.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.69000 DelPhi exited at 09:25:23 16.695u 0.469s 0:17.47 98.1% 0+0k 0+0io 0pf+0w