Sat Oct 8 18:47:30 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 Sat Oct 8 2011 at 18:47:30 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6331702 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): -32.11000 17.55700 ymin,ymax (A): -23.78000 23.20500 zmin,zma (A): -11.44600 44.77900 x,y,z range (A): 49.66700 46.98500 56.22500 scale (grids/A): 0.6331702 object centre (A): -7.276501 -0.2874994 16.66650 number of atom coordinates read : 2581 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.54737 89.19480 89.42145 assigned negative charge : -387.4045 centred at (gu) : 88.46194 89.22919 89.30700 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6895 nv = 96 ne = 84 npr = 53318 no. pairs analyzed = 53318 no. exposed pairs = 2976 no. arc points = 21312 no. surface atoms = 1005 nbur = 1576 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3905 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.2800000 number of dielectric boundary points 3293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2205 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8379 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0792350E-09 1.3956809E-08 midg,1,midg; midg,igrid,midg 9.7967154E-09 1.4040122E-09 1,midg,midg; igrid,midg,midg -4.7343574E-09 9.5875281E-09 gauss-seidel spectral radius is 0.9870747 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 18:47:31 rms-change max change #iterations 0.1401561 20.34615 at 10iterations 1.3544953E-02 1.924103 at 20iterations 1.3328486E-03 0.1906750 at 30iterations 1.2686448E-04 1.8270493E-02 at 40iterations 1.2530806E-05 1.7809868E-03 at 50iterations finished qdiffx linear iterations at : 18:47:33 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.2530806E-05 1.7809868E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 18:47:34 3.090u 0.144s 0:03.57 90.4% 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 18:47:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.899511 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): -32.11000 17.55700 ymin,ymax (A): -23.78000 23.20500 zmin,zma (A): -11.44600 44.77900 x,y,z range (A): 49.66700 46.98500 56.22500 scale (grids/A): 1.899511 object centre (A): -7.276501 -0.2874994 16.66650 number of atom coordinates read : 2581 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.64147 87.58389 88.26385 assigned negative charge : -387.4045 centred at (gu) : 85.38550 87.68729 87.92086 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21312 grid for indexing accessible points = 1.400000 m= 27450 mr = 52512 m= 4351 mr = 20784 m= 247 mr = 2776 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2463 time to turn everything in is 0.5100000 number of dielectric boundary points 30399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19305 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) : 0.6331702 object centre at (A) : -7.276501 -0.2874994 16.66650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3702823E-02 2.4454173E-02 midg,1,midg; midg,igrid,midg 1.4203969E-02 3.6996207E-03 1,midg,midg; igrid,midg,midg -4.3167300E-03 3.5494868E-02 gauss-seidel spectral radius is 0.9986234 estimated iterations to convergence 214 setup time was (sec) 0.7800000 now iterating at: 18:47:35 rms-change max change #iterations 4.223771 174.0998 at 10iterations 1.972412 65.18377 at 20iterations 0.9221034 28.87923 at 30iterations 0.4313855 15.35595 at 40iterations 0.2008914 6.769972 at 50iterations 9.4042964E-02 3.117517 at 60iterations 4.3977804E-02 1.359211 at 70iterations 2.0572839E-02 0.6681619 at 80iterations 9.5877238E-03 0.2883091 at 90iterations 4.4838707E-03 0.1451511 at 100iterations 2.0937666E-03 7.0484161E-02 at 110iterations 9.7873714E-04 3.2474518E-02 at 120iterations finished qdiffx linear iterations at : 18:47:41 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 9.7873714E-04 3.2474518E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 18:47:41 6.962u 0.170s 0:07.40 96.3% 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 8 2011 at 18:47:41 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 459 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.849266 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): -32.11000 17.55700 ymin,ymax (A): -23.78000 23.20500 zmin,zma (A): -11.44600 44.77900 x,y,z range (A): 49.66700 46.98500 56.22500 scale (grids/A): 2.849266 object centre (A): -7.276501 -0.2874994 16.66650 number of atom coordinates read : 2581 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 83.46227 86.37577 87.39574 assigned negative charge : -387.4045 centred at (gu) : 83.07817 86.53092 86.88138 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 172420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21312 grid for indexing accessible points = 1.400000 m= 88851 mr = 126840 m= 32468 mr = 74073 m= 7770 mr = 26529 m= 1152 mr = 5984 m= 62 mr = 787 m= 0 mr = 29 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 8266 time to turn everything in is 1.260000 number of dielectric boundary points 68481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 19631 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) : 1.899511 object centre at (A) : -7.276501 -0.2874994 16.66650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1149427 0.3344311 midg,1,midg; midg,igrid,midg 0.1686242 1.9292643E-02 1,midg,midg; igrid,midg,midg -1.4187391E-02 0.4456297 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 1.540000 now iterating at: 18:47:43 rms-change max change #iterations 9.808759 391.2515 at 10iterations 5.683252 140.5906 at 20iterations 3.274968 60.70016 at 30iterations 1.882385 36.79638 at 40iterations 1.080420 20.55260 at 50iterations 0.6205415 11.43788 at 60iterations 0.3554514 6.760750 at 70iterations 0.2038715 4.058228 at 80iterations 0.1167603 2.135324 at 90iterations 6.6798352E-02 1.258053 at 100iterations 3.8301345E-02 0.7461205 at 110iterations 2.1914605E-02 0.3896790 at 120iterations 1.2536552E-02 0.2240257 at 130iterations 7.1561956E-03 0.1260452 at 140iterations 4.1020289E-03 7.5653076E-02 at 150iterations 2.3469452E-03 4.2797089E-02 at 160iterations 1.3460938E-03 3.1454086E-02 at 170iterations 7.6939550E-04 1.4926910E-02 at 180iterations finished qdiffx linear iterations at : 18:47:53 total time elapsed so far: 10.97000 # loops : 180 mean,max change (kT/e) : 7.6939550E-04 1.4926910E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.14000 DelPhi exited at 18:47:53 11.143u 0.193s 0:11.60 97.6% 0+0k 0+0io 0pf+0w