Mon Oct 10 17:07:13 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 17:07:13 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5133974 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): -16.75100 36.16200 ymin,ymax (A): -32.64400 31.29900 zmin,zma (A): -3.826000 65.51600 x,y,z range (A): 52.91300 63.94300 69.34200 scale (grids/A): 0.5133974 object centre (A): 9.705502 -0.6725006 30.84500 number of atom coordinates read : 4291 total number of charged atoms : 4047 net assigned charge : 4.700026 assigned positive charge : 637.5714 centred at (gu) : 90.47137 90.82966 87.52477 assigned negative charge : -632.8751 centred at (gu) : 90.32026 90.87069 87.52248 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7096 nv = 96 ne = 84 npr = 87756 no. pairs analyzed = 87756 no. exposed pairs = 5537 no. arc points = 37758 no. surface atoms = 1847 nbur = 2444 mkacc time = 0.1900000 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 = 1.652000 m= 249 mr = 3624 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3624 ## 522 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2918905E-10 4.2958647E-11 midg,1,midg; midg,igrid,midg 1.4418738E-10 -4.0386493E-11 1,midg,midg; igrid,midg,midg -2.8310670E-10 5.1456028E-10 gauss-seidel spectral radius is 0.9805614 estimated iterations to convergence 59 setup time was (sec) 0.6200000 now iterating at: 17:07:14 rms-change max change #iterations 6.7409448E-02 11.36293 at 10iterations 3.9254008E-03 0.6430969 at 20iterations 5.0358014E-04 7.4856400E-02 at 30iterations 1.8287935E-04 3.3186853E-02 at 40iterations 7.5698874E-05 1.4401913E-02 at 50iterations finished qdiffx linear iterations at : 17:07:16 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 7.5698874E-05 1.4401913E-02 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 17:07:17 3.226u 0.142s 0:03.88 86.5% 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 17:07:17 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.540192 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): -16.75100 36.16200 ymin,ymax (A): -32.64400 31.29900 zmin,zma (A): -3.826000 65.51600 x,y,z range (A): 52.91300 63.94300 69.34200 scale (grids/A): 1.540192 object centre (A): 9.705502 -0.6725006 30.84500 number of atom coordinates read : 4291 total number of charged atoms : 4047 net assigned charge : 4.700026 assigned positive charge : 637.5714 centred at (gu) : 91.41281 92.48801 82.57319 assigned negative charge : -632.8751 centred at (gu) : 90.96056 92.61181 82.56715 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 80330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37758 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 22647 mr = 54783 m= 1886 mr = 14849 m= 40 mr = 751 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 0.6100000 number of dielectric boundary points 34517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 514 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 30516 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) : 0.5133974 object centre at (A) : 9.705502 -0.6725006 30.84500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9687992E-03 1.1187331E-02 midg,1,midg; midg,igrid,midg -1.9692064E-03 -8.1275646E-03 1,midg,midg; igrid,midg,midg -3.4872098E-03 1.1879482E-02 gauss-seidel spectral radius is 0.9980852 estimated iterations to convergence 182 setup time was (sec) 0.8700000 now iterating at: 17:07:18 rms-change max change #iterations 3.589223 152.0198 at 10iterations 1.455365 51.55675 at 20iterations 0.5923976 20.59883 at 30iterations 0.2409571 9.383538 at 40iterations 9.7997122E-02 3.401531 at 50iterations 4.0086184E-02 1.337107 at 60iterations 1.6301377E-02 0.5418816 at 70iterations 6.7163091E-03 0.2233582 at 80iterations 2.7721673E-03 8.7747574E-02 at 90iterations 1.1770295E-03 4.0939331E-02 at 100iterations 5.2747101E-04 1.8196106E-02 at 110iterations 2.6546160E-04 9.1152191E-03 at 120iterations finished qdiffx linear iterations at : 17:07:24 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 2.6546160E-04 9.1152191E-03 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 17:07:25 7.458u 0.220s 0:08.04 95.3% 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 17:07:25 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4291 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.310288 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): -16.75100 36.16200 ymin,ymax (A): -32.64400 31.29900 zmin,zma (A): -3.826000 65.51600 x,y,z range (A): 52.91300 63.94300 69.34200 scale (grids/A): 2.310288 object centre (A): 9.705502 -0.6725006 30.84500 number of atom coordinates read : 4291 total number of charged atoms : 4047 net assigned charge : 4.700026 assigned positive charge : 637.5714 centred at (gu) : 92.11904 93.73151 78.85956 assigned negative charge : -632.8751 centred at (gu) : 91.44085 93.91761 78.85054 start vw surface at 0.1900000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 187084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37758 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81643 mr = 134303 m= 20016 mr = 63420 m= 2572 mr = 14184 m= 130 mr = 1521 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 1882 time to turn everything in is 1.330000 number of dielectric boundary points 77982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 32285 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) : 1.540192 object centre at (A) : 9.705502 -0.6725006 30.84500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1247464 0.3005060 midg,1,midg; midg,igrid,midg -9.6873410E-02 -0.1944583 1,midg,midg; igrid,midg,midg -4.8792847E-02 0.1787798 gauss-seidel spectral radius is 0.9991423 estimated iterations to convergence 270 setup time was (sec) 1.620000 now iterating at: 17:07:27 rms-change max change #iterations 9.703457 285.2264 at 10iterations 5.526228 137.1889 at 20iterations 3.121616 75.49377 at 30iterations 1.755053 43.48534 at 40iterations 0.9842418 23.43333 at 50iterations 0.5488972 12.22564 at 60iterations 0.3058585 6.800313 at 70iterations 0.1696523 4.260955 at 80iterations 9.4316058E-02 2.285019 at 90iterations 5.2219898E-02 1.116600 at 100iterations 2.8889950E-02 0.6304855 at 110iterations 1.6001394E-02 0.3420153 at 120iterations 8.8519631E-03 0.1934271 at 130iterations 4.9002464E-03 0.1108932 at 140iterations 2.7096113E-03 5.3562164E-02 at 150iterations 1.5065704E-03 3.1099319E-02 at 160iterations 8.4246666E-04 1.7646551E-02 at 170iterations 4.7671702E-04 1.0806084E-02 at 180iterations finished qdiffx linear iterations at : 17:07:37 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 4.7671702E-04 1.0806084E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 17:07:37 11.541u 0.234s 0:12.19 96.5% 0+0k 0+0io 0pf+0w