Thu Feb 2 02:26:57 PST 2012 #!/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 Thu Feb 2 2012 at 02:26:57 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 ! Automatically converted by prot2crg.py # of charge parameter records: 957 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 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: 0.5585189 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 0.5585189 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2803 total number of charged atoms : 2727 net assigned charge : 1.500008 assigned positive charge : 413.2773 centred at (gu) : 88.82164 89.12720 90.62437 assigned negative charge : -411.7785 centred at (gu) : 88.68993 89.19990 90.53645 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5994 nv = 96 ne = 84 npr = 54226 no. pairs analyzed = 54226 no. exposed pairs = 3803 no. arc points = 27194 no. surface atoms = 1272 nbur = 1531 mkacc time = 0.1100000 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= 225 mr = 2963 m= 2 mr = 8 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 0.2500000 number of dielectric boundary points 3250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2839 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 7717 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0537347E-10 1.1666175E-09 midg,1,midg; midg,igrid,midg 1.0605233E-09 -4.4756762E-10 1,midg,midg; igrid,midg,midg -1.5363147E-09 1.0616404E-09 gauss-seidel spectral radius is 0.9834637 estimated iterations to convergence 64 setup time was (sec) 0.4500000 now iterating at: 02:26:58 rms-change max change #iterations 7.5781755E-02 12.78251 at 10iterations 5.4460512E-03 0.8689098 at 20iterations 4.1389090E-04 6.3863754E-02 at 30iterations 4.0677518E-05 6.1874390E-03 at 40iterations 6.3015345E-06 9.5367432E-04 at 50iterations finished qdiffx linear iterations at : 02:27:01 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 6.3015345E-06 9.5367432E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 02:27:01 3.550u 0.181s 0:04.16 89.6% 0+0k 0+45936io 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 Thu Feb 2 2012 at 02:27:02 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 ! Automatically converted by prot2crg.py # of charge parameter records: 957 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 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: 1.675557 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 1.675557 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2803 total number of charged atoms : 2727 net assigned charge : 1.500008 assigned positive charge : 413.2773 centred at (gu) : 86.46392 87.38095 91.87234 assigned negative charge : -411.7785 centred at (gu) : 86.06959 87.59949 91.60893 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 65480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27194 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19805 mr = 43081 m= 2184 mr = 13231 m= 73 mr = 1086 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 504 time to turn everything in is 0.4000000 number of dielectric boundary points 30139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 21015 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) : 0.5585189 object centre at (A) : 5.560500 -5.153999 25.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7198047E-02 8.2730008E-03 midg,1,midg; midg,igrid,midg 1.4474062E-03 -8.7129977E-03 1,midg,midg; igrid,midg,midg -5.8196229E-03 1.7413361E-02 gauss-seidel spectral radius is 0.9982765 estimated iterations to convergence 191 setup time was (sec) 0.6000000 now iterating at: 02:27:02 rms-change max change #iterations 3.344844 154.3723 at 10iterations 1.423658 64.26789 at 20iterations 0.6074311 23.13034 at 30iterations 0.2586565 9.052023 at 40iterations 0.1102762 3.914127 at 50iterations 4.6984099E-02 1.690260 at 60iterations 1.9992087E-02 0.7462621 at 70iterations 8.5307434E-03 0.2942133 at 80iterations 3.6350009E-03 0.1310635 at 90iterations 1.5558096E-03 5.5773735E-02 at 100iterations 6.6112092E-04 2.3345947E-02 at 110iterations 2.8297392E-04 9.5672607E-03 at 120iterations finished qdiffx linear iterations at : 02:27:10 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.8297392E-04 9.5672607E-03 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 02:27:10 7.986u 0.215s 0:08.47 96.6% 0+0k 0+45280io 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 Thu Feb 2 2012 at 02:27:10 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 ! Automatically converted by prot2crg.py # of charge parameter records: 957 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 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: 2.513335 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 2.513335 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2803 total number of charged atoms : 2727 net assigned charge : 1.500008 assigned positive charge : 413.2773 centred at (gu) : 84.69562 86.07117 92.80841 assigned negative charge : -411.7785 centred at (gu) : 84.10433 86.39930 92.41344 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 152160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27194 grid for indexing accessible points = 1.400000 m= 67815 mr = 106056 m= 19893 mr = 52508 m= 3442 mr = 14637 m= 268 mr = 2280 m= 5 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 1657 time to turn everything in is 1.020000 number of dielectric boundary points 67983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 21797 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) : 1.675557 object centre at (A) : 5.560500 -5.153999 25.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4434812 0.2113881 midg,1,midg; midg,igrid,midg 2.0395432E-02 -0.1043297 1,midg,midg; igrid,midg,midg -9.2066117E-02 0.2696805 gauss-seidel spectral radius is 0.9991703 estimated iterations to convergence 274 setup time was (sec) 1.250000 now iterating at: 02:27:12 rms-change max change #iterations 8.645373 387.8250 at 10iterations 4.929611 123.8137 at 20iterations 2.795238 63.21367 at 30iterations 1.575701 35.26261 at 40iterations 0.8838461 22.48336 at 50iterations 0.4959932 10.43336 at 60iterations 0.2768895 5.999966 at 70iterations 0.1547000 3.289017 at 80iterations 8.6260349E-02 1.927155 at 90iterations 4.8010975E-02 1.021865 at 100iterations 2.6770035E-02 0.5708660 at 110iterations 1.4847745E-02 0.3148923 at 120iterations 8.2721263E-03 0.1610551 at 130iterations 4.5981072E-03 9.4726563E-02 at 140iterations 2.5584139E-03 5.2486420E-02 at 150iterations 1.4197091E-03 3.0370712E-02 at 160iterations 7.8858092E-04 1.6664505E-02 at 170iterations 4.3941112E-04 8.9149475E-03 at 180iterations finished qdiffx linear iterations at : 02:27:23 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 4.3941112E-04 8.9149475E-03 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 02:27:23 12.717u 0.228s 0:13.25 97.5% 0+0k 0+45272io 0pf+0w