Mon Oct 10 17:05:03 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 Mon Oct 10 2011 at 17:05:03 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: 236 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= 5.0000001E-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 : 3.500014 assigned positive charge : 378.4209 centred at (gu) : 89.46554 88.80740 90.85427 assigned negative charge : -374.9215 centred at (gu) : 89.53134 88.86587 90.76264 start vw surface at 0.1000000 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 = 8.9999996E-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 = 0.1000000 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 -2.0703999E-09 7.8981133E-09 midg,1,midg; midg,igrid,midg 6.4112018E-09 -6.4009065E-10 1,midg,midg; igrid,midg,midg 5.9331176E-09 -1.0822739E-09 gauss-seidel spectral radius is 0.9861470 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 17:05:03 rms-change max change #iterations 0.1137471 18.13207 at 10iterations 9.9962950E-03 1.940493 at 20iterations 9.0120255E-04 0.1450572 at 30iterations 8.0131795E-05 1.1909485E-02 at 40iterations 7.9545043E-06 1.1978149E-03 at 50iterations finished qdiffx linear iterations at : 17:05:06 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.9545043E-06 1.1978149E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:05:07 3.448u 0.171s 0:04.18 86.3% 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 Mon Oct 10 2011 at 17:05:07 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: 236 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= 5.0000001E-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 : 3.500014 assigned positive charge : 378.4209 centred at (gu) : 88.39609 86.42177 92.56213 assigned negative charge : -374.9215 centred at (gu) : 88.59383 86.59724 92.28773 start vw surface at 9.0000004E-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 = 0.1700000 no. cavity mid-points inaccessible to solvent = 505 time to turn everything in is 0.3600000 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 0.4400000 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 -1.4894426E-02 2.7365157E-02 midg,1,midg; midg,igrid,midg 2.1257127E-02 1.0657008E-02 1,midg,midg; igrid,midg,midg 3.2069986E-03 -8.5740881E-03 gauss-seidel spectral radius is 0.9985409 estimated iterations to convergence 208 setup time was (sec) 0.5900000 now iterating at: 17:05:08 rms-change max change #iterations 3.853098 167.1295 at 10iterations 1.753456 63.93538 at 20iterations 0.8013371 26.42509 at 30iterations 0.3645422 11.92782 at 40iterations 0.1664354 6.013702 at 50iterations 7.5423099E-02 2.588367 at 60iterations 3.4593489E-02 1.161810 at 70iterations 1.5795248E-02 0.5519371 at 80iterations 7.1801487E-03 0.2281542 at 90iterations 3.2822574E-03 0.1007421 at 100iterations 1.4950153E-03 4.7492981E-02 at 110iterations 6.8232435E-04 2.1680832E-02 at 120iterations finished qdiffx linear iterations at : 17:05:15 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 6.8232435E-04 2.1680832E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 17:05:16 8.378u 0.243s 0:09.22 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 Mon Oct 10 2011 at 17:05:16 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: 236 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 : 3.500014 assigned positive charge : 378.4209 centred at (gu) : 87.59402 84.63256 93.84318 assigned negative charge : -374.9215 centred at (gu) : 87.89066 84.89585 93.43147 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 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 -0.2063268 0.5961202 midg,1,midg; midg,igrid,midg 0.1749399 0.1177795 1,midg,midg; igrid,midg,midg 5.3149112E-02 -0.1245182 gauss-seidel spectral radius is 0.9992467 estimated iterations to convergence 288 setup time was (sec) 1.140000 now iterating at: 17:05:18 rms-change max change #iterations 9.335452 325.6379 at 10iterations 5.432320 124.2790 at 20iterations 3.147862 70.69418 at 30iterations 1.814003 39.07407 at 40iterations 1.044043 20.62431 at 50iterations 0.6005768 12.52123 at 60iterations 0.3439142 6.822106 at 70iterations 0.1970924 4.006800 at 80iterations 0.1128459 2.108709 at 90iterations 6.4679943E-02 1.271667 at 100iterations 3.7004091E-02 0.7153069 at 110iterations 2.1152442E-02 0.4056053 at 120iterations 1.2080813E-02 0.2686462 at 130iterations 6.9036679E-03 0.1243892 at 140iterations 3.9503537E-03 8.3179474E-02 at 150iterations 2.2556488E-03 4.5641899E-02 at 160iterations 1.2892876E-03 2.6062012E-02 at 170iterations 7.3655514E-04 1.4140606E-02 at 180iterations finished qdiffx linear iterations at : 17:05:29 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 7.3655514E-04 1.4140606E-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 17:05:30 12.758u 0.239s 0:14.00 92.7% 0+0k 0+0io 0pf+0w