Mon Oct 10 17:05:31 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 17:05:31 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 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: 0.6111483 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): 20.66100 71.56400 ymin,ymax (A): 8.950001 59.29500 zmin,zma (A): -32.46400 25.78700 x,y,z range (A): 50.90300 50.34500 58.25100 scale (grids/A): 0.6111483 object centre (A): 46.11250 34.12250 -3.338500 number of atom coordinates read : 2560 total number of charged atoms : 2424 net assigned charge : 3.500013 assigned positive charge : 380.0209 centred at (gu) : 89.47331 88.79865 90.84756 assigned negative charge : -376.5215 centred at (gu) : 89.54185 88.85071 90.75560 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6624 nv = 96 ne = 84 npr = 50547 no. pairs analyzed = 50547 no. exposed pairs = 3453 no. arc points = 24766 no. surface atoms = 1160 nbur = 1400 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3384 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2483 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1011315E-09 7.9327638E-09 midg,1,midg; midg,igrid,midg 6.0307936E-09 -4.0020989E-10 1,midg,midg; igrid,midg,midg 6.0923431E-09 -1.2159509E-09 gauss-seidel spectral radius is 0.9861470 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 17:05:31 rms-change max change #iterations 0.1155592 18.36454 at 10iterations 1.0180307E-02 1.970951 at 20iterations 9.1938744E-04 0.1365738 at 30iterations 8.2468723E-05 1.2546539E-02 at 40iterations 8.5237216E-06 1.3017654E-03 at 50iterations finished qdiffx linear iterations at : 17:05:34 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 8.5237216E-06 1.3017654E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 17:05:35 3.404u 0.188s 0:04.20 85.2% 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 17:05:35 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 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: 1.833445 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): 20.66100 71.56400 ymin,ymax (A): 8.950001 59.29500 zmin,zma (A): -32.46400 25.78700 x,y,z range (A): 50.90300 50.34500 58.25100 scale (grids/A): 1.833445 object centre (A): 46.11250 34.12250 -3.338500 number of atom coordinates read : 2560 total number of charged atoms : 2424 net assigned charge : 3.500013 assigned positive charge : 380.0209 centred at (gu) : 88.41950 86.39552 92.54199 assigned negative charge : -376.5215 centred at (gu) : 88.62536 86.55176 92.26664 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24766 grid for indexing accessible points = 1.400000 m= 24956 mr = 47694 m= 3669 mr = 17724 m= 179 mr = 2118 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 505 time to turn everything in is 0.3500000 number of dielectric boundary points 32616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 18993 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) : 0.6111483 object centre at (A) : 46.11250 34.12250 -3.338500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4965176E-02 2.7432108E-02 midg,1,midg; midg,igrid,midg 2.0684034E-02 1.1067247E-02 1,midg,midg; igrid,midg,midg 3.6850052E-03 -9.1429790E-03 gauss-seidel spectral radius is 0.9985409 estimated iterations to convergence 208 setup time was (sec) 0.5700000 now iterating at: 17:05:36 rms-change max change #iterations 3.877812 167.1295 at 10iterations 1.764510 66.11757 at 20iterations 0.8063822 27.59235 at 30iterations 0.3669082 11.88227 at 40iterations 0.1675353 6.049755 at 50iterations 7.5948551E-02 2.612106 at 60iterations 3.4818150E-02 1.165098 at 70iterations 1.5896242E-02 0.5541039 at 80iterations 7.2265319E-03 0.2305727 at 90iterations 3.3061146E-03 9.9928856E-02 at 100iterations 1.5054151E-03 4.8636436E-02 at 110iterations 6.8692531E-04 2.2265434E-02 at 120iterations finished qdiffx linear iterations at : 17:05:43 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 6.8692531E-04 2.2265434E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 17:05:43 7.875u 0.231s 0:08.45 95.8% 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 17:05:43 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2560 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: 2.750167 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): 20.66100 71.56400 ymin,ymax (A): 8.950001 59.29500 zmin,zma (A): -32.46400 25.78700 x,y,z range (A): 50.90300 50.34500 58.25100 scale (grids/A): 2.750167 object centre (A): 46.11250 34.12250 -3.338500 number of atom coordinates read : 2560 total number of charged atoms : 2424 net assigned charge : 3.500013 assigned positive charge : 380.0209 centred at (gu) : 87.62914 84.59318 93.81297 assigned negative charge : -376.5215 centred at (gu) : 87.93795 84.82760 93.39984 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 165163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24766 grid for indexing accessible points = 1.400000 m= 80649 mr = 116297 m= 28499 mr = 64462 m= 6514 mr = 22437 m= 820 mr = 4625 m= 36 mr = 457 m= 0 mr = 8 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1647 time to turn everything in is 0.9000000 number of dielectric boundary points 73395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19382 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) : 1.833445 object centre at (A) : 46.11250 34.12250 -3.338500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2067673 0.5971926 midg,1,midg; midg,igrid,midg 0.1692367 0.1220008 1,midg,midg; igrid,midg,midg 5.9837349E-02 -0.1307798 gauss-seidel spectral radius is 0.9992467 estimated iterations to convergence 288 setup time was (sec) 1.130000 now iterating at: 17:05:45 rms-change max change #iterations 9.394135 325.6380 at 10iterations 5.463921 124.2932 at 20iterations 3.166853 68.61243 at 30iterations 1.824470 39.25285 at 40iterations 1.050081 20.65665 at 50iterations 0.6039114 12.93421 at 60iterations 0.3457446 6.834975 at 70iterations 0.1981518 4.067909 at 80iterations 0.1134480 2.121262 at 90iterations 6.5015063E-02 1.265415 at 100iterations 3.7199352E-02 0.7204742 at 110iterations 2.1264380E-02 0.3945541 at 120iterations 1.2142501E-02 0.2723694 at 130iterations 6.9395858E-03 0.1250858 at 140iterations 3.9709285E-03 8.4486008E-02 at 150iterations 2.2675500E-03 4.5227051E-02 at 160iterations 1.2958345E-03 2.6702881E-02 at 170iterations 7.4046629E-04 1.3946533E-02 at 180iterations finished qdiffx linear iterations at : 17:05:56 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 7.4046629E-04 1.3946533E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 17:05:57 12.766u 0.246s 0:13.43 96.7% 0+0k 0+0io 0pf+0w