Sat Oct 15 12:53:40 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 15 2011 at 12:53:40 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 209 has a net charge of 0.5140 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 0.6030321 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): 27.20700 81.35400 ymin,ymax (A): -44.98600 14.04900 zmin,zma (A): -15.92200 35.61500 x,y,z range (A): 54.14700 59.03500 51.53700 scale (grids/A): 0.6030321 object centre (A): 54.28050 -15.46850 9.846500 number of atom coordinates read : 2625 total number of charged atoms : 2506 net assigned charge : 2.096024 assigned positive charge : 389.2108 centred at (gu) : 88.87576 90.22859 89.54137 assigned negative charge : -387.1158 centred at (gu) : 88.86368 90.15734 89.59087 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6583 nv = 96 ne = 84 npr = 51095 no. pairs analyzed = 51095 no. exposed pairs = 3651 no. arc points = 26167 no. surface atoms = 1209 nbur = 1416 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3308 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3300000 number of dielectric boundary points 3616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2621 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2673255E-09 -9.0285923E-10 midg,1,midg; midg,igrid,midg -1.7894548E-09 4.0034003E-09 1,midg,midg; igrid,midg,midg 6.2667244E-10 1.1399245E-09 gauss-seidel spectral radius is 0.9857836 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 12:53:41 rms-change max change #iterations 0.1070276 14.25413 at 10iterations 9.2984615E-03 1.454048 at 20iterations 7.9275033E-04 0.1176703 at 30iterations 6.8356356E-05 1.0517120E-02 at 40iterations 5.9307231E-06 8.8930130E-04 at 50iterations finished qdiffx linear iterations at : 12:53:46 total time elapsed so far: 5.550000 # loops : 50 mean,max change (kT/e) : 5.9307231E-06 8.8930130E-04 energy calculations done at 5.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.720000 DelPhi exited at 12:53:46 5.728u 0.449s 0:06.60 93.3% 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 15 2011 at 12:53:46 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 209 has a net charge of 0.5140 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 1.809096 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): 27.20700 81.35400 ymin,ymax (A): -44.98600 14.04900 zmin,zma (A): -15.92200 35.61500 x,y,z range (A): 54.14700 59.03500 51.53700 scale (grids/A): 1.809096 object centre (A): 54.28050 -15.46850 9.846500 number of atom coordinates read : 2625 total number of charged atoms : 2506 net assigned charge : 2.096024 assigned positive charge : 389.2108 centred at (gu) : 86.62669 90.68546 88.62331 assigned negative charge : -387.1158 centred at (gu) : 86.59089 90.47208 88.77251 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70563 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26167 grid for indexing accessible points = 1.400000 m= 24779 mr = 46319 m= 3829 mr = 17408 m= 196 mr = 2184 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 0.6100000 number of dielectric boundary points 33409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19582 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) : 0.6030321 object centre at (A) : 54.28050 -15.46850 9.846500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7626682E-02 1.0035997E-02 midg,1,midg; midg,igrid,midg 6.9164666E-03 1.4035949E-03 1,midg,midg; igrid,midg,midg -7.4611064E-03 -6.5464508E-03 gauss-seidel spectral radius is 0.9985164 estimated iterations to convergence 206 setup time was (sec) 1.030000 now iterating at: 12:53:48 rms-change max change #iterations 3.809082 174.3960 at 10iterations 1.708787 60.44553 at 20iterations 0.7713702 26.36497 at 30iterations 0.3491878 12.94709 at 40iterations 0.1584134 6.303457 at 50iterations 7.1647391E-02 2.828466 at 60iterations 3.2380432E-02 1.011637 at 70iterations 1.4602592E-02 0.5197496 at 80iterations 6.6567138E-03 0.2135258 at 90iterations 3.0118891E-03 0.1001472 at 100iterations 1.3631032E-03 4.6621323E-02 at 110iterations 6.1855261E-04 1.9927979E-02 at 120iterations finished qdiffx linear iterations at : 12:54:09 total time elapsed so far: 13.64000 # loops : 120 mean,max change (kT/e) : 6.1855261E-04 1.9927979E-02 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.81000 DelPhi exited at 12:54:10 13.817u 0.540s 0:23.77 60.3% 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 15 2011 at 12:54:10 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 209 has a net charge of 0.5140 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 2.713645 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): 27.20700 81.35400 ymin,ymax (A): -44.98600 14.04900 zmin,zma (A): -15.92200 35.61500 x,y,z range (A): 54.14700 59.03500 51.53700 scale (grids/A): 2.713645 object centre (A): 54.28050 -15.46850 9.846500 number of atom coordinates read : 2625 total number of charged atoms : 2506 net assigned charge : 2.096024 assigned positive charge : 389.2108 centred at (gu) : 84.93996 91.02789 87.93479 assigned negative charge : -387.1158 centred at (gu) : 84.88633 90.70815 88.15891 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 162822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26167 grid for indexing accessible points = 1.400000 m= 79348 mr = 112938 m= 29009 mr = 62756 m= 6795 mr = 22516 m= 769 mr = 4775 m= 43 mr = 433 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 476 time to turn everything in is 1.590000 number of dielectric boundary points 75346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 20040 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) : 1.809096 object centre at (A) : 54.28050 -15.46850 9.846500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1386531 0.1181229 midg,1,midg; midg,igrid,midg 0.2659558 -1.1086688E-02 1,midg,midg; igrid,midg,midg -0.1614168 -0.1344951 gauss-seidel spectral radius is 0.9992364 estimated iterations to convergence 286 setup time was (sec) 2.040000 now iterating at: 12:54:15 rms-change max change #iterations 9.337455 353.2368 at 10iterations 5.419191 125.7523 at 20iterations 3.121708 73.72045 at 30iterations 1.795176 39.16254 at 40iterations 1.028159 20.86979 at 50iterations 0.5875107 11.47077 at 60iterations 0.3355049 6.508331 at 70iterations 0.1912305 3.971312 at 80iterations 0.1089031 2.073919 at 90iterations 6.1933201E-02 1.240776 at 100iterations 3.5308678E-02 0.7025719 at 110iterations 2.0095490E-02 0.3929811 at 120iterations 1.1434785E-02 0.2261810 at 130iterations 6.5117306E-03 0.1233349 at 140iterations 3.6945229E-03 6.6326141E-02 at 150iterations 2.1039713E-03 3.9379358E-02 at 160iterations 1.1965181E-03 2.3802221E-02 at 170iterations 6.8052142E-04 1.2636662E-02 at 180iterations finished qdiffx linear iterations at : 12:54:37 total time elapsed so far: 23.03000 # loops : 180 mean,max change (kT/e) : 6.8052142E-04 1.2636662E-02 energy calculations done at 23.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.21000 DelPhi exited at 12:54:38 23.217u 0.575s 0:27.73 85.7% 0+0k 0+0io 0pf+0w