Sat Oct 8 11:35:08 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 Sat Oct 8 2011 at 11:35:08 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 !!! WARNING: HIR 388 has a net charge of 0.5140 !!! WARNING: HIR 402 has a net charge of 0.5140 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: 0.5708055 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 0.5708055 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.971998 assigned positive charge : 273.9562 centred at (gu) : 91.98106 88.68901 88.50996 assigned negative charge : -275.9285 centred at (gu) : 91.97967 88.69115 88.70096 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4527 nv = 96 ne = 84 npr = 43500 no. pairs analyzed = 43500 no. exposed pairs = 2710 no. arc points = 19357 no. surface atoms = 919 nbur = 1135 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= 227 mr = 2177 m= 0 mr = 18 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2900000 number of dielectric boundary points 2559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1876 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1876152E-09 -1.5994542E-09 midg,1,midg; midg,igrid,midg -4.3068124E-10 -2.6636951E-10 1,midg,midg; igrid,midg,midg -2.2411800E-10 -5.1618165E-10 gauss-seidel spectral radius is 0.9840972 estimated iterations to convergence 65 setup time was (sec) 0.5600000 now iterating at: 11:35:08 rms-change max change #iterations 6.8569653E-02 13.92555 at 10iterations 5.8903461E-03 1.042324 at 20iterations 1.3035113E-03 0.2672749 at 30iterations 5.4720190E-04 0.1142654 at 40iterations 2.3861617E-04 4.9926758E-02 at 50iterations finished qdiffx linear iterations at : 11:35:12 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 2.3861617E-04 4.9926758E-02 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 11:35:12 4.022u 0.254s 0:04.73 90.2% 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 Sat Oct 8 2011 at 11:35:12 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 !!! WARNING: HIR 388 has a net charge of 0.5140 !!! WARNING: HIR 402 has a net charge of 0.5140 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: 1.712417 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 1.712417 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.971998 assigned positive charge : 273.9562 centred at (gu) : 95.94328 86.06715 85.53024 assigned negative charge : -275.9285 centred at (gu) : 95.93938 86.07379 86.10309 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 49311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19357 grid for indexing accessible points = 1.400000 m= 15508 mr = 31782 m= 2001 mr = 10448 m= 45 mr = 1043 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 850 time to turn everything in is 0.4600000 number of dielectric boundary points 23589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14997 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) : 0.5708055 object centre at (A) : -9.177502 -6.357000 49.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6528837E-02 -1.0855809E-02 midg,1,midg; midg,igrid,midg -2.9711176E-03 -8.5432717E-04 1,midg,midg; igrid,midg,midg -3.3587927E-04 -5.0104404E-04 gauss-seidel spectral radius is 0.9982592 estimated iterations to convergence 190 setup time was (sec) 0.7500000 now iterating at: 11:35:13 rms-change max change #iterations 2.789103 176.9728 at 10iterations 1.180707 55.01426 at 20iterations 0.4985490 22.14503 at 30iterations 0.2130395 8.668068 at 40iterations 9.0547338E-02 3.443168 at 50iterations 3.8748771E-02 1.501907 at 60iterations 1.6711403E-02 0.7093887 at 70iterations 7.6470836E-03 0.3541355 at 80iterations 3.8834289E-03 0.1844826 at 90iterations 2.3150383E-03 0.1074963 at 100iterations 1.5854379E-03 7.0577621E-02 at 110iterations 1.1690130E-03 5.1010132E-02 at 120iterations finished qdiffx linear iterations at : 11:35:22 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 1.1690130E-03 5.1010132E-02 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.060000 DelPhi exited at 11:35:22 9.058u 0.288s 0:09.66 96.5% 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 Sat Oct 8 2011 at 11:35:22 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 !!! WARNING: HIR 388 has a net charge of 0.5140 !!! WARNING: HIR 402 has a net charge of 0.5140 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: 2.568625 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): -32.49700 14.14200 ymin,ymax (A): -26.16100 13.44700 zmin,zma (A): 17.86100 80.22900 x,y,z range (A): 46.63900 39.60800 62.36800 scale (grids/A): 2.568625 object centre (A): -9.177502 -6.357000 49.04500 number of atom coordinates read : 2054 total number of charged atoms : 1927 net assigned charge : -1.971998 assigned positive charge : 273.9562 centred at (gu) : 98.91489 84.10068 83.29540 assigned negative charge : -275.9285 centred at (gu) : 98.90926 84.11080 84.15464 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 114376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19357 grid for indexing accessible points = 1.400000 m= 51574 mr = 78471 m= 16622 mr = 39632 m= 3189 mr = 12383 m= 238 mr = 2172 m= 2 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 3060 time to turn everything in is 1.110000 number of dielectric boundary points 53220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 15408 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) : 1.712417 object centre at (A) : -9.177502 -6.357000 49.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3190503 -0.1560951 midg,1,midg; midg,igrid,midg -4.2455953E-02 -1.4445648E-03 1,midg,midg; igrid,midg,midg -4.1195662E-03 -1.2664223E-02 gauss-seidel spectral radius is 0.9991370 estimated iterations to convergence 269 setup time was (sec) 1.420000 now iterating at: 11:35:24 rms-change max change #iterations 7.049784 337.7926 at 10iterations 3.950987 107.0312 at 20iterations 2.193276 53.69887 at 30iterations 1.218824 30.20070 at 40iterations 0.6785157 16.55523 at 50iterations 0.3742425 9.036215 at 60iterations 0.2074544 5.901794 at 70iterations 0.1142231 2.634508 at 80iterations 6.3009702E-02 1.779591 at 90iterations 3.4828331E-02 0.8006344 at 100iterations 1.9175952E-02 0.4599934 at 110iterations 1.0623520E-02 0.2446709 at 120iterations 5.9442627E-03 0.1612854 at 130iterations 3.3897287E-03 8.2962036E-02 at 140iterations 2.0092048E-03 5.3369522E-02 at 150iterations 1.2741277E-03 3.4503937E-02 at 160iterations 8.8596606E-04 2.6031494E-02 at 170iterations 6.7371625E-04 1.7700195E-02 at 180iterations finished qdiffx linear iterations at : 11:35:37 total time elapsed so far: 14.48000 # loops : 180 mean,max change (kT/e) : 6.7371625E-04 1.7700195E-02 energy calculations done at 14.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.66000 DelPhi exited at 11:35:37 14.661u 0.306s 0:15.32 97.6% 0+0k 0+0io 0pf+0w