Tue Oct 11 04:53:11 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 Tue Oct 11 2011 at 04:53:11 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 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: 0.6850106 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): -2.964000 49.00600 ymin,ymax (A): -10.16700 36.18200 zmin,zma (A): -18.61900 18.17500 x,y,z range (A): 51.97000 46.34900 36.79400 scale (grids/A): 0.6850106 object centre (A): 23.02100 13.00750 -0.2219992 number of atom coordinates read : 2112 total number of charged atoms : 1966 net assigned charge : 5.945010 assigned positive charge : 322.7331 centred at (gu) : 91.02248 91.35347 90.03402 assigned negative charge : -316.7881 centred at (gu) : 90.99900 91.20141 90.06703 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6392 nv = 96 ne = 84 npr = 43816 no. pairs analyzed = 43816 no. exposed pairs = 2399 no. arc points = 16428 no. surface atoms = 825 nbur = 1287 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3703 m= 2 mr = 49 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 0.2600000 number of dielectric boundary points 2996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1532 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7796468E-08 1.8437454E-08 midg,1,midg; midg,igrid,midg -1.3252762E-08 9.5946703E-08 1,midg,midg; igrid,midg,midg 1.7477280E-08 4.3077261E-08 gauss-seidel spectral radius is 0.9888939 estimated iterations to convergence 77 setup time was (sec) 0.4700000 now iterating at: 04:53:11 rms-change max change #iterations 0.1790543 24.89599 at 10iterations 2.1227764E-02 3.407606 at 20iterations 2.4992912E-03 0.3525867 at 30iterations 3.1784258E-04 4.4490814E-02 at 40iterations 4.8984472E-05 7.2536469E-03 at 50iterations finished qdiffx linear iterations at : 04:53:14 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 4.8984472E-05 7.2536469E-03 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 04:53:14 3.022u 0.157s 0:03.67 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 Tue Oct 11 2011 at 04:53:14 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 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: 2.055032 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): -2.964000 49.00600 ymin,ymax (A): -10.16700 36.18200 zmin,zma (A): -18.61900 18.17500 x,y,z range (A): 51.97000 46.34900 36.79400 scale (grids/A): 2.055032 object centre (A): 23.02100 13.00750 -0.2219992 number of atom coordinates read : 2112 total number of charged atoms : 1966 net assigned charge : 5.945010 assigned positive charge : 322.7331 centred at (gu) : 93.06731 94.06050 90.10214 assigned negative charge : -316.7881 centred at (gu) : 92.99701 93.60403 90.20113 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16428 grid for indexing accessible points = 1.400000 m= 25728 mr = 49737 m= 4357 mr = 19290 m= 318 mr = 2732 m= 11 mr = 134 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 27650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 15572 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) : 0.6850106 object centre at (A) : 23.02100 13.00750 -0.2219992 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5802696E-02 9.1192583E-03 midg,1,midg; midg,igrid,midg -4.6556454E-02 4.7876094E-02 1,midg,midg; igrid,midg,midg 3.3455126E-02 8.9614592E-02 gauss-seidel spectral radius is 0.9987550 estimated iterations to convergence 224 setup time was (sec) 0.7500000 now iterating at: 04:53:15 rms-change max change #iterations 4.400823 187.8405 at 10iterations 2.135572 72.43428 at 20iterations 1.035391 33.95033 at 30iterations 0.5039206 15.40554 at 40iterations 0.2446441 7.792156 at 50iterations 0.1189441 3.486456 at 60iterations 5.7728957E-02 1.773495 at 70iterations 2.8000487E-02 0.8741302 at 80iterations 1.3682096E-02 0.4204788 at 90iterations 6.6425065E-03 0.2035828 at 100iterations 3.2552178E-03 0.1000214 at 110iterations 1.6027722E-03 5.7487488E-02 at 120iterations finished qdiffx linear iterations at : 04:53:21 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 1.6027722E-03 5.7487488E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 04:53:22 6.879u 0.165s 0:07.36 95.5% 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 Tue Oct 11 2011 at 04:53:22 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: 348 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 has a net charge of -0.0940 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: 3.082548 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): -2.964000 49.00600 ymin,ymax (A): -10.16700 36.18200 zmin,zma (A): -18.61900 18.17500 x,y,z range (A): 51.97000 46.34900 36.79400 scale (grids/A): 3.082548 object centre (A): 23.02100 13.00750 -0.2219992 number of atom coordinates read : 2112 total number of charged atoms : 1966 net assigned charge : 5.945010 assigned positive charge : 322.7331 centred at (gu) : 94.60091 96.09062 90.15326 assigned negative charge : -316.7881 centred at (gu) : 94.49549 95.40619 90.30173 start vw surface at 0.1400000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 159805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16428 grid for indexing accessible points = 1.400000 m= 82882 mr = 119909 m= 30840 mr = 68842 m= 7755 mr = 24876 m= 1286 mr = 5853 m= 151 mr = 873 m= 4 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 62279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 15728 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) : 2.055032 object centre at (A) : 23.02100 13.00750 -0.2219992 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1407879 6.5551333E-02 midg,1,midg; midg,igrid,midg -0.6254699 0.4331199 1,midg,midg; igrid,midg,midg 0.1818899 1.522993 gauss-seidel spectral radius is 0.9992719 estimated iterations to convergence 292 setup time was (sec) 1.800000 now iterating at: 04:53:24 rms-change max change #iterations 9.925701 448.2359 at 10iterations 5.798325 117.6776 at 20iterations 3.380499 76.33374 at 30iterations 1.970131 35.27847 at 40iterations 1.141686 21.88530 at 50iterations 0.6643870 12.23432 at 60iterations 0.3856476 7.385159 at 70iterations 0.2236649 4.037821 at 80iterations 0.1298814 2.347614 at 90iterations 7.5225681E-02 1.351936 at 100iterations 4.3652408E-02 0.7986336 at 110iterations 2.5392795E-02 0.4911795 at 120iterations 1.4850581E-02 0.2748442 at 130iterations 8.7726656E-03 0.1534863 at 140iterations 5.2517503E-03 0.1021032 at 150iterations 3.2086885E-03 6.2927246E-02 at 160iterations 2.0330281E-03 4.1221619E-02 at 170iterations 1.3491790E-03 2.9401779E-02 at 180iterations finished qdiffx linear iterations at : 04:53:33 total time elapsed so far: 11.21000 # loops : 180 mean,max change (kT/e) : 1.3491790E-03 2.9401779E-02 energy calculations done at 11.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 04:53:34 11.394u 0.172s 0:11.99 96.4% 0+0k 0+0io 0pf+0w