Sun Oct 9 12:46:20 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 Sun Oct 9 2011 at 12:46:20 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 = 2395 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: 0.6943767 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): -6.050000 44.04500 ymin,ymax (A): -1.008000 50.26100 zmin,zma (A): 34.33300 75.88300 x,y,z range (A): 50.09500 51.26900 41.55000 scale (grids/A): 0.6943767 object centre (A): 18.99750 24.62650 55.10800 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 2.500025 assigned positive charge : 369.0231 centred at (gu) : 89.55343 88.90374 89.40253 assigned negative charge : -366.5235 centred at (gu) : 89.55197 88.70512 89.34840 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7632 nv = 96 ne = 84 npr = 48589 no. pairs analyzed = 48589 no. exposed pairs = 2917 no. arc points = 20218 no. surface atoms = 976 nbur = 1419 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 492 mr = 4278 m= 5 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1922 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7600459E-09 3.5443215E-08 midg,1,midg; midg,igrid,midg -8.8650964E-08 8.0785803E-08 1,midg,midg; igrid,midg,midg 1.7504119E-08 1.5897108E-08 gauss-seidel spectral radius is 0.9892219 estimated iterations to convergence 78 setup time was (sec) 0.5400000 now iterating at: 12:46:20 rms-change max change #iterations 0.2016308 28.16241 at 10iterations 2.4616014E-02 3.893355 at 20iterations 3.3396531E-03 0.4460258 at 30iterations 6.6188135E-04 0.1113434 at 40iterations 1.9091145E-04 3.1822205E-02 at 50iterations finished qdiffx linear iterations at : 12:46:23 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.9091145E-04 3.1822205E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 12:46:24 3.411u 0.144s 0:03.82 92.9% 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 Sun Oct 9 2011 at 12:46:24 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 = 2395 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: 2.083130 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): -6.050000 44.04500 ymin,ymax (A): -1.008000 50.26100 zmin,zma (A): 34.33300 75.88300 x,y,z range (A): 50.09500 51.26900 41.55000 scale (grids/A): 2.083130 object centre (A): 18.99750 24.62650 55.10800 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 2.500025 assigned positive charge : 369.0231 centred at (gu) : 88.65992 86.71063 88.20742 assigned negative charge : -366.5235 centred at (gu) : 88.65566 86.11517 88.04510 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81652 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20218 grid for indexing accessible points = 1.400000 m= 31271 mr = 57339 m= 5672 mr = 23390 m= 541 mr = 3672 m= 12 mr = 284 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 103 time to turn everything in is 0.6100000 number of dielectric boundary points 34461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17870 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) : 0.6943767 object centre at (A) : 18.99750 24.62650 55.10800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1769406E-03 4.8141886E-02 midg,1,midg; midg,igrid,midg -7.5534366E-02 1.7586401E-02 1,midg,midg; igrid,midg,midg 4.8394226E-02 1.2954210E-03 gauss-seidel spectral radius is 0.9988253 estimated iterations to convergence 231 setup time was (sec) 0.9000000 now iterating at: 12:46:25 rms-change max change #iterations 4.935514 254.2607 at 10iterations 2.432778 89.71210 at 20iterations 1.204550 38.76173 at 30iterations 0.5971999 17.49068 at 40iterations 0.2955487 8.916485 at 50iterations 0.1467388 4.238657 at 60iterations 7.2368093E-02 1.988403 at 70iterations 3.6158916E-02 1.044652 at 80iterations 1.8041728E-02 0.6026878 at 90iterations 9.0610320E-03 0.2771511 at 100iterations 4.5648199E-03 0.1430206 at 110iterations 2.3887842E-03 7.2834015E-02 at 120iterations finished qdiffx linear iterations at : 12:46:31 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 2.3887842E-03 7.2834015E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 12:46:32 7.745u 0.180s 0:08.19 96.7% 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 Sun Oct 9 2011 at 12:46:32 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 = 2395 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: 3.124695 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): -6.050000 44.04500 ymin,ymax (A): -1.008000 50.26100 zmin,zma (A): 34.33300 75.88300 x,y,z range (A): 50.09500 51.26900 41.55000 scale (grids/A): 3.124695 object centre (A): 18.99750 24.62650 55.10800 number of atom coordinates read : 2395 total number of charged atoms : 2253 net assigned charge : 2.500025 assigned positive charge : 369.0231 centred at (gu) : 87.98974 85.06583 87.31090 assigned negative charge : -366.5235 centred at (gu) : 87.98345 84.17268 87.06756 start vw surface at 0.1700000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 188714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20218 grid for indexing accessible points = 1.400000 m= 98759 mr = 138673 m= 38113 mr = 81633 m= 10412 mr = 30784 m= 2200 mr = 7876 m= 264 mr = 1688 m= 6 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 281 time to turn everything in is 1.980000 number of dielectric boundary points 77650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 18024 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) : 2.083130 object centre at (A) : 18.99750 24.62650 55.10800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7335667E-02 0.4998865 midg,1,midg; midg,igrid,midg -0.7659430 0.4055162 1,midg,midg; igrid,midg,midg 0.5287644 -0.1780155 gauss-seidel spectral radius is 0.9992968 estimated iterations to convergence 298 setup time was (sec) 2.280000 now iterating at: 12:46:34 rms-change max change #iterations 11.05976 359.7599 at 10iterations 6.546064 121.2600 at 20iterations 3.860221 69.21729 at 30iterations 2.280187 42.23366 at 40iterations 1.345592 23.30961 at 50iterations 0.7886171 14.50027 at 60iterations 0.4633800 8.871178 at 70iterations 0.2717341 5.324421 at 80iterations 0.1590935 2.877579 at 90iterations 9.3326628E-02 1.652366 at 100iterations 5.4731179E-02 0.8717003 at 110iterations 3.2202333E-02 0.5331268 at 120iterations 1.9142395E-02 0.3247147 at 130iterations 1.1484299E-02 0.2329578 at 140iterations 7.0720557E-03 0.1345024 at 150iterations 4.5309053E-03 8.7585449E-02 at 160iterations 3.0541320E-03 6.9221497E-02 at 170iterations 2.1979874E-03 5.0117493E-02 at 180iterations finished qdiffx linear iterations at : 12:46:45 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 2.1979874E-03 5.0117493E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 12:46:45 12.842u 0.170s 0:13.44 96.8% 0+0k 0+0io 0pf+0w