Tue Nov 22 14:14:44 PST 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 Tue Nov 22 2011 at 14:14:49 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 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: 0.5955667 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): -24.53100 35.24400 ymin,ymax (A): -19.16700 20.74400 zmin,zma (A): -2.836000 39.86600 x,y,z range (A): 59.77500 39.91100 42.70200 scale (grids/A): 0.5955667 object centre (A): 5.356502 0.7884998 18.51500 number of atom coordinates read : 2171 total number of charged atoms : 1865 net assigned charge : 4.000007 assigned positive charge : 298.0129 centred at (gu) : 89.71626 90.45258 90.09387 assigned negative charge : -294.0132 centred at (gu) : 89.75076 90.53764 90.21434 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4853 nv = 96 ne = 84 npr = 40277 no. pairs analyzed = 40277 no. exposed pairs = 2437 no. arc points = 17233 no. surface atoms = 829 nbur = 1342 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 226 mr = 2688 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5849 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2640704E-09 -1.4797815E-09 midg,1,midg; midg,igrid,midg 3.1797225E-09 -6.4559169E-10 1,midg,midg; igrid,midg,midg 2.4771230E-09 6.2422684E-10 gauss-seidel spectral radius is 0.9853619 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 14:14:52 rms-change max change #iterations 9.0816937E-02 17.71950 at 10iterations 7.4948296E-03 1.426584 at 20iterations 6.1266683E-04 0.1015282 at 30iterations 5.1888921E-05 1.0232925E-02 at 40iterations 4.4398703E-06 9.1934204E-04 at 50iterations finished qdiffx linear iterations at : 14:15:00 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 4.4398703E-06 9.1934204E-04 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 14:15:02 3.272u 0.166s 0:14.10 24.3% 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 Tue Nov 22 2011 at 14:15:05 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 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: 1.786700 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): -24.53100 35.24400 ymin,ymax (A): -19.16700 20.74400 zmin,zma (A): -2.836000 39.86600 x,y,z range (A): 59.77500 39.91100 42.70200 scale (grids/A): 1.786700 object centre (A): 5.356502 0.7884998 18.51500 number of atom coordinates read : 2171 total number of charged atoms : 1865 net assigned charge : 4.000007 assigned positive charge : 298.0129 centred at (gu) : 89.14838 91.35772 90.28188 assigned negative charge : -294.0132 centred at (gu) : 89.25238 91.61301 90.64306 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 19008 mr = 36218 m= 2422 mr = 14389 m= 92 mr = 1400 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 440 time to turn everything in is 0.3600000 number of dielectric boundary points 21791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14516 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) : 0.5955667 object centre at (A) : 5.356502 0.7884998 18.51500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9583743E-03 -3.5140784E-03 midg,1,midg; midg,igrid,midg 4.4897008E-03 -9.9356708E-05 1,midg,midg; igrid,midg,midg 3.0768413E-02 1.9758966E-02 gauss-seidel spectral radius is 0.9983791 estimated iterations to convergence 197 setup time was (sec) 0.6200000 now iterating at: 14:15:10 rms-change max change #iterations 3.210427 145.5932 at 10iterations 1.404231 56.32611 at 20iterations 0.6134476 25.66365 at 30iterations 0.2681628 11.20184 at 40iterations 0.1171943 5.037329 at 50iterations 5.0990351E-02 1.952083 at 60iterations 2.2414735E-02 0.8895378 at 70iterations 9.7785434E-03 0.3809233 at 80iterations 4.2762659E-03 0.1532478 at 90iterations 1.8785388E-03 7.0465088E-02 at 100iterations 8.1913272E-04 3.1463623E-02 at 110iterations 3.5891929E-04 1.3351440E-02 at 120iterations finished qdiffx linear iterations at : 14:15:28 total time elapsed so far: 6.480000 # loops : 120 mean,max change (kT/e) : 3.5891929E-04 1.3351440E-02 energy calculations done at 6.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.650000 DelPhi exited at 14:15:29 6.656u 0.155s 0:25.22 26.9% 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 Tue Nov 22 2011 at 14:15:32 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2171 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: 2.680050 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): -24.53100 35.24400 ymin,ymax (A): -19.16700 20.74400 zmin,zma (A): -2.836000 39.86600 x,y,z range (A): 59.77500 39.91100 42.70200 scale (grids/A): 2.680050 object centre (A): 5.356502 0.7884998 18.51500 number of atom coordinates read : 2171 total number of charged atoms : 1865 net assigned charge : 4.000007 assigned positive charge : 298.0129 centred at (gu) : 88.72256 92.03660 90.42268 assigned negative charge : -294.0132 centred at (gu) : 88.87860 92.41949 90.96470 start vw surface at 0.1200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 120700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 62475 mr = 87312 m= 21567 mr = 52135 m= 4079 mr = 17480 m= 400 mr = 2953 m= 13 mr = 250 m= 0 mr = 2 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1484 time to turn everything in is 0.8800000 number of dielectric boundary points 49102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 14917 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) : 1.786700 object centre at (A) : 5.356502 0.7884998 18.51500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1002165 -4.1763164E-02 midg,1,midg; midg,igrid,midg 3.9519917E-02 6.0458877E-03 1,midg,midg; igrid,midg,midg 0.3615890 0.2093180 gauss-seidel spectral radius is 0.9991688 estimated iterations to convergence 274 setup time was (sec) 1.150000 now iterating at: 14:15:38 rms-change max change #iterations 7.730678 298.3414 at 10iterations 4.324782 108.1606 at 20iterations 2.414162 56.25031 at 30iterations 1.341799 28.82195 at 40iterations 0.7459484 16.53833 at 50iterations 0.4127550 9.044991 at 60iterations 0.2292412 4.754930 at 70iterations 0.1269583 2.659256 at 80iterations 7.0276663E-02 1.553834 at 90iterations 3.8987763E-02 0.8458090 at 100iterations 2.1614872E-02 0.4752975 at 110iterations 1.1993125E-02 0.2649183 at 120iterations 6.6567264E-03 0.1440268 at 130iterations 3.6886986E-03 8.0682755E-02 at 140iterations 2.0427385E-03 4.4107676E-02 at 150iterations 1.1342788E-03 2.5923729E-02 at 160iterations 6.2741153E-04 1.6369343E-02 at 170iterations 3.4739522E-04 7.4481964E-03 at 180iterations finished qdiffx linear iterations at : 14:16:06 total time elapsed so far: 10.51000 # loops : 180 mean,max change (kT/e) : 3.4739522E-04 7.4481964E-03 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 14:16:09 10.697u 0.157s 0:37.58 28.8% 0+0k 0+0io 0pf+0w